Anything I should know about updating?

Just replace the exe?

Yes, just replace the exe. It's backward compatible.

You can however move mTES4.exe and mTES4.ini into their own folder now if you want.

Updated fine and seems to work!

Thanks

... you're not helping my mod greed issue which I thought I had under control.

[edit] with the method of having the shortcuts on desktop that point to the active Oblivion folder - they keep loosing their icons.

I am so this is where youv been I willl also be an early aaptor but not quite this early I have been reading through the whole thread & it's really exciting

Well it works - I mean it is so cool - it takes opening this simple little app and then clicking on a clone then setting to active and there you have a whole install swapped out. Like 3 seconds. The basic functions are all there and the new delete clone function offers a pop up window where you chose what to get rid of from just undoing the install as a clone to full deletion.

I'd recommend a few things before using. Really read this over is the first.

Next if you have a back up or new install to load onto the computer do that so when making clones it will be of a clean install. I went ahead and tweaked the vanilla install I had with LAA exe, PyFFI meshes bsa, several ini tweaks I always do, shader 3.0 for ati, etc. So with each clone I make that is all done.

Just back up your normal install (and save game profile folder and app data folder) and place in that space the simpler one or reinstall and then each clone will be simple and ready to go. Otherwise each clone will be what you've already modded again. Not good as my main install is over 30 gigs.

I would think that anyone who mods and plays or even just playtests for modders would find this a great help.

My current install is Nehrim only & not that advanced, so I might just clean it all out & start fresh using this & mash installer rather than OBMM , but I will watch developments for a few days

If you simply rename all the current folders - like put a +++before the names of the folders then you should be able to install Oblivion again in the same spot. You could assign the new install as the basic clone then rename its game folder to something like Oblivion_Base Install (what I did). When you import a clone you can have the new clone called whatever you like (and rename it again later).

For Nehrim just move the Nehrim game folder up to the same directory as Oblivion (and other clones). Then import it. But you will see - it not at all that complex or scary.

You mean when you switch clones, your shortcuts vanish?
I put mine onto my taskbar, I don't have any problems with them there.

No just the icon for the shortcut - hmm but maybe it is because i changed the icon - maybe I should store the icons in a centrally located position that does not shift.

Icons on apps are a royal pain to change with Vista - icons on shortcuts not so bad but maybe if the path gets changed as to where the icon is that effects the shortcut.

I think you mean Bash, not Mash. Bash is for Oblivion, Mash is for Morrowind.
But cheers to you for taking the next step! Bash is a pretty big learning curve, but you won't regret it.

If you need any help or are unsure how to get started with mTES4 or Bash, just ask.

I just thought of a minor bug. A variation of the duplicate clone name bug.

If you have both Oblivion and Fallout3 installed, you can potentially create a new clone for one game (Eg. Oblivion) that is named the same as the active clone for the other game (Eg. Fallout3).
Attempting to switch the active clone for Fallout3 would then fail because a clone folder already exists with the same name.

I have used bash back when I did my last big install of Oblivion a couple of years ago but then OBMM was the main contender & wrye installers tab was the new kid. My recent experience has been with Mash, and it's the first time iv'e used the installers tab & I loved it. Ofcourse in Morrowind there are less competetors no OBMM for a start, well someone did a port but it has had a serious thumbs down from the community so Iv'e never installed it. Nehrim has totally pulled me away from a new install of morrowind I was in the process of building. I was never able to get into the main quest in Oblivion so never finished it. It was possible to ignore the main quest for a long time in Morrowind in fact you were positivly encouraged to do so. In Oblivion after my first few games I used to aviod going anywhere near Kvatch to the extent of swimming along the coast to avoid even the chance that I might trigger the main quest. All those Oblivion gates appearing all over the place & all essentially the same. One little touch I really like in Nehrim is the great big collection of standing stones none of which seem to actually do anything. I'm expecting to find a collection of miniature oblivion gates stashed somewhere in the game sometime. So far I'm enjoying Nehrim allthough I'm already starting to look for an Economy mod & I think I would like to see some changes to Alchemy I think it is a serious risk for the balance of my game. Iv'e allways thought that the best potions should come for the professionals & should be really expensive. At level 12 with no brought skill ups & an Alchemy skill of 25, I can already make potions that are better than anything i can buy & that have 3 or 4 effects so that I can swallow more power up's.

Anyway thats enough I'm at serious risk of hijacking your thread here, time I got off here & installed the lovely little tool allthough it looks i'd better get myself a lot bigger hard disk before I do Beebee

I've been on such a roll getting this app fleshed out, why stop now huh?

Upcoming fixes and features:- Bug fix for possible duplicate named clones if you have more than one supported game installed. Affected Import, Copy and Rename features.- New minimize to tray option. Hovering over the tray icon will show the currently active game and clone.- New r-click menu for the tray icon allows you to conveniently switch games or clones.- New custom autolaunch tools settings for each clone.If an autolaunch tool is configured for a clone, when you switch to that clone, by default mTES4 will ask you if you want to launch it.Additionally there is also a setting to have mTES4 always autolaunch without asking.- New Launch Tools dialog. Allows you to choose what tool you want to launch.- New Custom Tool settings can be configured in mTES4.ini and the _mTES4 (*).ini tag files.Custom tools will be listed in the Launch Tools dialog.You can define custom tools that will be listed for all games and clones and/or you can define custom tools that will only be listed for a specific game or clone.

Before this new version can be readied for release, I need to know what common tools should be supported for Fallout3.
I need specifics. IE the filename, path and if there are any special arguments.
I believe the obse equiv for fallout3 is fose_loader.exe? same arguments?

Here is mTES4's list of predefined tools and their relative paths: (all but OBSE/FOSE are configurable in the ini files)
.\obse_loader.exe
.\obse_loader.exe -editor
.\Mopy\Wrye Bash launcher.pyw
.\OblivionModManager.exe
.\Oblivion.exe
.\OblvionLauncher.exe
.\TESConstructionSet.exe
.\TES4Edit.exe
.\TES4Gecko.exe -Xmx1024m
.\Tools\TES4Files.exe
.\TES4LodGen.exe

I installed Gecko outside the Oblivion folder and only have a shortcut there - will that still work?

as for Fallout - yes fose_loader.exe

Wrye Flash/Gary Bash has the same Mopy folder set up.

The trickier part is FO3edit - there are many in the F3 'community' who are under the delusion that a special function of FO3edit called masterupdate is necessary. With Fallout 3 when official patches were still being released patch #5 presented a serious bug for modders - it made it so that only esm would work when adding plugins. It took Bethesda several weeks maybe even a few months to undo that with the next patch. In the meantime Elminster came up with a function of edit called masterupdate. What it does is add the flag to each plugin that makes it a master (bash and other utilities can do that too) ... this just does the entire load order at once.

You use that by renaming edit to FO3MasterUpdate.exe and then to undo that you name it to FO3MasterRestore.exe - for my install I put these in seperate folders and apparently FO3edit does not require being in any specific folder either. I'd bet you would be safe just putting in the readme to have them in the Fallout3 directory.

I myself don't use Masterupdate and found no benefit with it. In fact I think it a pain in the [censored]. But things are different over there. They recommend using FO3edit to make merged patches and most mods are released as dirty as you can imagine. I think Wrye would have labeled them bash deniers.

All this though reminds me of a feature I'd like to request for http://www.gamesas.com/index.php?/topic/1119410-fo3edit-for-new-vegas/.

Your TES4gecko shortcut would not be detected as a predefined tool, you would have to customize the entry to point to the shortcut or the real path.
Pretty much the same as Bash.

With the exception of obse and fose, the predefined tools are merely defaults and will only be displayed in the tools dialog if the tool exists.
So I'm just looking for defaults here. If a user has deviated from the suggested setup, it's up to them to custom configure the tools.

The predefined ones can be customized via the ini files. Plus you can add your own.

You lost me on the FO3MasterUpdate explanation. Sounds like I would not predefine those.

What is the actual filename for Wrye Flash. Wrye Flash Launcher.pyw?

Let me pose my original request slightly different.
What in that list will not work with Fallout3?
What is the replacements?
What other tools should be supported, for either Oblivion or Fallout3?

I don't recall gecko having a suggested install locale, but this is not a real issue for me ... I'll either reinstall or just not care as with bash.

You could easily ... it is just that there are three versions of FO3edit to consider:
FO3edit.exe
FO3MasterUpdate.exe
FO3MasterRestore.exe ... while I'm not an advocate of masterupdating a load order there are some who are fanatical that it works and should be done and would call me trolling for even suggesting that it does nothing much. So if it is not included then you bet it will be a feature request.

Of course all that may be moot once New Vegas comes out and FO3edit gets another version - they may have figured out how to keep it all one exe - that thread I linked is the best source of info on the next version right now.

Actually so far it is still the same as bash: Wrye Bash Launcher.pyw

Well the construction set is called the GECK and it's exe named: Geck.exe which I think most put in the Fallout3 directory next to the fallout3.exe

http://fallout3nexus.com/downloads/file.php?id=5104 is a simple mod combining tool - never used it, but hear it is like Gecko.

You might find more http://www.gamesas.com/?showtopic=972430&hl=

v0.5b is ready!

Download: http://gaticus.iwireweb.com/download/mTES4%20v0.5.0b%20r75.zip

Version 0.5.0b Changelog

- New minimize to tray option. Hovering over the tray icon will show the currently active game and clone.- New r-click menu for the tray icon allows you to conveniently switch games or clones.- New custom AutoLaunch tools settings for each clone.- New Launch Tools dialog. Allows you to choose what tool you want to launch.- New Custom Tool settings can be configured in mTES4.ini and the _mTES4 (*).ini tag files.- bug fix for possible duplicate named clones if you have more than one supported game installed.Affected Import, Copy and Rename features

See the http://www.gamesas.com/index.php?/topic/1119357-wipz-mtes4-manager/page__view__findpost__p__16453179 for info about the new features.
In particular, there is 3 new sections describing the AutoLaunch feature, the Launch Tools and how to customize them.

If you are already using mTES4, in order to take advantage of the predefined tools just delete your existing mTES4.ini file so a new one will be generated.
The only settings you will lose are what game and what clone are active.
mTES4 can automatically determine the active clone anyways.

Sorry if this has been asked a million times, but I have been reading the web last 5h (to make sure I set up my SSD drive correctly), so I′m just gona ask:


How do safely go about making a second installation of Oblivion? I have a working installation, now I want a second one, and plan on managing them with this great looking tool. My aim is to have both modding and gaming setup, separately

(the current one should be the modding one, so I want to keep sure I don′t lose my files - the second one is supposed to be a clean install on my new SSD, on which I plan on installing mods and test my own mods before releasing)


Thanks for replays to my stupid question!


EDIT: Hmm...I′m starting to have concerns about my plan...I need to have all the copies on the same drive, right? I may run into space issues...the whole plan was to have the playing clone on the new drive...

To make a second installation, just use mTES4. [EDIT] Sorry, Psymon is right.
You should not create clones from an already modified and used installation. See the guide I wrote in the post below.

You are right though that mTES4 requires you to have both copies installed on the same drive.

Technically, you can't install Oblivion twice. What mTES4 does for you is replace your game folders with the other copy.
The reason that mTES4 requires the copies to be in the same place on the same drive is because if you were to swap them from different drives it would require
copying/moving your existing game folders to your other drive (which will take about 5 minutes for a vanilla install),
then copying/moving your duplicate game folders back to the other drives (taking another 5 minutes).

If you don't have enough space on your existing drive, maybe you could move your current Oblivion install onto your new drive when you get it?

On a side note:
In my personal opinion, SSD's are not worth the extra cash unless you have a specific, optimized use for (a small) one. They are still a relatively new technology and pricey.
One great use of SSD's would be to put your windows installation onto it, your windows swap file or disk caches for things like Photoshop.
If you plan to use your SSD for general purposes while your system is still installed on an HDD, I'm afraid you won't see the speed improvement you might expect because windows itself will slow you down.
Don't get me wrong. SSD is really great but it's advantages only truly shine when you install your system on one.
Either way, SSD's are alot more robust and require far less power. The best part of all is that they never have to be defragmented though!
SSD's will always run at peak performance, no matter how full it is or organized the data is. HDD's get slower the more stuff you put on them and the more disorganized the data becomes.

You can get hybrid drives now. They seem very promising. They are like regular HDD's but they have a tiny builtin SSD that is used to automatically optimize storage of small and frequently used files.

[EDIT]
I just reread your post after replying and realized you already have an SSD. My advice is still applicable to you and anyone else who might be interested in buying an SSD though, so I won't strike any text.

Skycaptain

I would recommend you only make clones of the a vanilla or lightly modded game so that any new clones will be light weight. I renamed my main bloat modded game then put in a fresh one to make it my base install that I can then clone all I want.

For my root/main/base clone I just have the game with some tweaks I know I will always use (LAA exe, PyFFI meshes BSA, certain ini tweaks, etc).

One way to save space is to set the directory for installing OMODs and BAIN archives to another drive this will then leave only the game and what is installed on the drive.

I agree about SSDs - too little for too much. I heard good things about the WD 2TB 64 buffer drives though.

A Guide to Setting Up Multiple Copies of Oblivion using mTES4
So you have downloaded mTES4 and you want to set up multiple copies of Oblivion. Now what?

This guide assumes that you already have Oblivion installed.
Whether you have Oblivion installed yet or not, please read the whole guide first before doing anything, because you can save yourself some steps depending on your situation.
The instructions in this guide are generic for general use cases and not all instructions may be necessary depending on your situation and what you intend to use mTES4 for.

Yeah, yeah. I read through it all already. Let's get on with it.
If you have not run mTES4 yet. Do so now.
When mTES4 starts up it will detect your current Oblivion install and if it has not already been tagged as a clone, it will ask you to provide a name for it.
For the purposes of this guide, please name it 'Original Copy'. You can easily rename all your clones after you have completed this guide.

Once your install copy has been named, you will see it listed in the Detected Clones list.
At this point, mTES4 is not particularly useful, until you have established a second clone that you can switch to.

You should not create clone copies from an existing game install that has already been modded unless you want those mods and (associated glitches!) to carry over to your new clones! Instead, it is recommended that you establish a clean clone that you can make copies from.


So what is a clean clone then?
A clean clone is essentially a backup copy of Vanilla Oblivion, without any mods. The clean clone is used to create new copies which you can then modify how you wish.
You should never mod or play the clean clone with the exception of adding what you would consider essential changes that you want to be pre-installed in every new clone you make.

If you have SI and/or any of the DLC's, you may want to pre-install them, keeping in mind that ALL of your new clones will include those as well.

If it's not already, make sure your game is updated to the latest patch.

If there are things that you always want changed, you can pre-install those changes in your clean clone.
Remember though, that it's almost always easier to add any of these things to a new clone, than it is to remove them so decide carefully before including anything in your clean clone.
You are much better off not to pre-install anything, unless you are sure you will want it installed with ALL new clones.

You may like to install everything separately for each clone, but I suggest pre-installing the various Oblivion tools you use:
Tools such as Wrye Bash, OBMM, OBSE, TESCS, TES4Edit, TESGecko, etc, etc

Some examples of other types of things you might like to pre-install are:
- The Unofficial Oblivion Patches
- DarN UI (or whatever your preference is)
- Texture and mesh Replacers, such as QTP, Roberts Male Body, HGEC
- Game tweaking plugins such as TQP, Keychain, Cobl, MAO

Don't forget, if you have any doubt just don't pre-install anything.


Ok, so how do I make a clean clone?
Option A:
If you have just freshly installed Oblivion or if you have never modded your game, this is simple. Create a clean clone by copying your Original Copy.
Using mTES4, select your 'Original Copy' from the Detected Clones list. Click the Copy Clone button and name the new clone to 'Clean Copy'.
This will take a couple minutes while your game folder is copied, then you are done. That's it! Skip on to the next section of this guide.

Option B:
If your game has already been modded and you already have your own backup copy of a fresh installation. Import your backup.
To import an existing copy of the game as a new clone, the copy must reside in the same folder as your Oblivion install folder. All clones must be in the same place.
EG.
C:\Games\Oblivion
C:\Games\Clone1
C:\Games\Clone2

The clean clone will effectively be a backup of a fresh install, so you probably don't need to keep a separate backup copy anymore.
If your backup is not in the same location as the Oblivion installation, move or copy it there. Rename the folder to 'Clean Copy'
Using mTES4, click the Import Clone button. Select your Clean Copy folder. Now you can go to the next section of this guide.

Option C:
If you do not have a backup copy already and your game is already modded, you will need to reinstall the game so you can get a fresh copy.
Before you do this, you want to preserve your existing game. You can use mTES4 to create a backup, so you don't lose everything when you reinstall.
Create a New Folder in the same location as your Oblivion installation and name it 'Dummy Copy'.
EG.
C:\Games\Oblivion
C:\Games\Dummy Copy

Using mTES4, click Import Clone and choose the Dummy Copy folder.
You should now see both your 'Original Copy' and the 'Dummy Copy' listed in the Detected Clones list.
Select the Dummy Copy and click the Switch button. The Dummy Copy will move to the top of the list and should be the one in bold text signifying that it is the active clone.
Make sure the Dummy Copy is active and not your Original Copy or you will lose everything! Close mTES4.

Now using your game discs (or steam or what not), reinstall the game. Make sure you reinstall to the same location that it was before.

When the game installation is finished, open mTES4 again. It should still list the Dummy Copy and the Original Copy.
The Dummy Copy is now your fresh install, so select it, click the Rename button and change it to Clean Copy.

Now you should have your Original Copy and your new Clean Copy.

I have my clean clone, now what should I do?
By now, you should have two clones. Your Original Copy and a Clean Copy.

Reiterating something I already mentioned: You should never mod or play your clean clone.
The purpose of having a clean clone is for your convenience to make new clone copies from. If you mod or play the clean clone, it won't be clean anymore.
Keeping a clean clone does however require some extra diskspace (normally around 4 to 5gb depending on what you have pre-installed), so remember that this is all just recommendation. You certainly can go through the above steps again to create a new fresh copy.

Before you start making new clone copies from your clean clone, if you haven't done so already, take the time to prepare your clean clone by pre-installing your favorite 'essentials' that you know you will want in all of your new clones.
Refer to the section above about what a clean clone is for some suggestions.

Yes I have prepared my clean clone and pre-installed the things I want to be in every new clone. Can I start playing now?
Not quite yet. So far you only have your Original Copy (first install) and a fresh, Clean Copy. You want to preserve your Clean Copy (you should not play or mod it), so you should create a second playable now.

If you don't want to keep a clean clone for whatever reason, you can just use your new Clean Copy as your second install. Just rename your Clean Copy to something more descriptive.
Remember though, if you ever want to create an additional clone, you will need a fresh install and will have to go through the above steps again.

If you want to keep your clean clone (and you really should, unless you don't have the diskspace for it).
Using mTES4, select your Clean Copy from the Detected Clones list and click the Copy Clone button. Name your new clone however you like. Hopefully something descriptive depending on what you intend to use the clone for
Assuming your new clone will be used for modding, you might name it 'Modded Copy'.

Now that you have two playable clones: your Original Copy and your Modded Copy. You can use mTES4 to switch between them whenever you choose.

Alright, can I start playing NOW?
Yep, if you have followed the above instructions, you should now have two playable clones.
Just use mTES4 to Switch to the clone you want to be active and do your thing.

As long as you kept your clean clone, you can create new clones from it at any time by using mTES4.

Wait, I wanted to install Nehrim. I don't think this is going to work for me. What do I do now?
If all you want to use mTES4 for is to play Nehrim, you actually don't need to make a second playable clone, unless of course you want a second copy of Oblivion to mess with.

Instead, install Nehrim as you normally would and then import it to mTES4.
After Nehrim has been installed, it should be in a folder next to your \Oblivion folder named \SureAI\Nehrim.
EG.
C:\Program Files\Bethesda Softworks\Oblivion
C:\Program Files\Bethesda Softworks\SureAI\Nehrim

In order to be able to import any new clone, the game folder must be directly next to the \Oblivion folder. So you need to move the Nehrim folder from \SureAI\Nehrim to just \Nehrim.
EG.
C:\Program Files\Bethesda Softworks\Nehrim

Open mTES4, click the Import Clone button and select the Nehrim folder. Click OK and you are done.
You should now see at least your Original Copy and your Nehrim clones in the Detected Clones list.


Hold on, how come I've got so many different clones now!?
By this point you may have up to 4 clones!
Hopefully you have read through this guide before doing anything instead of just blindly following along and you really did want to have 4 clones!
If not then I suggest you read again. There is no harm in deleting the clones you don't want (from mTES4, don't just delete the folders), except that you may need to recreate them again later.


A few suggestions...
1. If you are are reading this guide, you most likely already have an idea of how it can be useful to have multiple clones of Oblivion.
Besides just having two different versions of the game to play, here are a few ways of using mTES4 that you may not have thought of:
i. If you are a modder, I don't need to tell you how handy it can be to have a separate clone just for development. I call them CS clones, because they invariably include the TESCS. You might even have several if you have several major projects. You could also have different test clones with different mod setups so you can see how your mods interact with others. For example, you might have a vanilla test clone and an SI clone, etc.
ii. If you are not a modder, you might have a test clone so you can easily try new mods without breaking your game.
iii. If you want to try any total conversions like Nehrim, you could have a separate clone for it, so you can still keep your Oblivion game and all the game settings will be separate.
iv. If you plan to add new mods to your existing game, you can create a clone copy as a backup. If the new mod makes a mess of things, simply switch to your backup.
(As I'm writing this, I'm realizing that creating a complete backup using mTES4 is not actually possible right now, since mTES4 will not copy your game settings. So ignore item #iv for the moment. Stay tuned)

2. If you have the opportunity to reinstall Oblivion, consider renaming the installation folder to something shorter that you can use as a prefix for all of your clones.
For example, I have renamed my installation folder to TES4 and all of my clones begin with TES4-.
This means that all of the folders sort alphabetically in windows explorer and are grouped together, making it much easier to see which folders are actually clone folders among other clutter.
Because the installation folder is named just TES4, it always comes first before the other clones in my folder listing.
For example:

Looks great - here are a few bits of feedback about what can be done with a clean copy.

Regarding the first clean clone - remember if you install even a tool then if that tool is ever updated then it will need to be updated for each clone and since that is the case I'd think that it might be better to do that fore each clone. Wrye Bash has been known to go through periods of frequent updates. Currently there have been a string of updates to http://www.tesnexus.com/downloads/file.php?id=32277. Likewise a http://www.gamesas.com/index.php?/topic/1119410-fo3edit-for-new-vegas/ is in the future. So I'd recommend not adding tools even OBSE which again is in stages for a new update. Also one may want a clone with different bash versions or OBSE versions.

Same goes for mods. UOP has seen a lot of updates lately thanks to Arthmoor. TQP just got an update. Since installers are being updated I would not recommend even mods, but then that is up to the user and if they prefer manual installing more power to them. One could of course do things like add the OBSE folder to the data folder.

These kinds of tweaks can be done to the basic install and are very handy:

Large Address Aware flag for the Oblivion.exe - more information found here: http://www.gamesas.com/index.php?/topic/1118450-oblivion-and-memory-usage/ ... Mostly for 64 OS users.

Altered BSA files - probably the most important is http://www.gamesas.com/index.php?/topic/1112284-inforelz-pyffi-python-file-format-interface/. But also decompressing the textures file and possibly splitting it. As described in the http://www.gamesas.com/?showtopic=881204&st=0&gopid=12871765&#entry12871765. Still others might prefer to repack their meshes and textures with favorite replacers.

I would recommend starting the game and even starting a character (don't have to save it) so that one could:
1. Set resolution as they usually like
2. map the controls as they usually like
3. Starting game also generates the renderInfo.txt which gives details about shaders. Some prefer to force Oblivion to use 3.0 shaders as described http://www.tweakguides.com/Oblivion_8.html. Or ATI users might prefer http://www.silgrad.com/wbb2/thread.php?goto=nextnewest&threadid=6886&sid=54f905e37983706cae6fc4e3f78a414e.
4. Starting game also generates the ini and while one can edit the default ini - I notices some entries that I change aren't on the default and I had to generate it to find them.

INI tweaks - here are a few I always do:
iShadowMapResolution=1024 http://www.uesp.net/wiki/Oblivion:Technical_Support#Crashes
bUseJoystick = 0 (having it at one is another known source of problems)
bAllowScreenShot=1 (take pictures)
bEnableBorderRegion=1 (removes the invisible border walls)
blocalmapshader=0 (local map becomes colored)
DlgFocus=3.5000 (Removes the really annoying 'all up in your face' closeness during dialogue as described http://amito.freehostia.com/Oblivion/OB-tips.htm#Oblivion.ini_File.)

If one wanted http://www.tesnexus.com/downloads/file.php?id=10724 without using Wrye Bash then that too.
.
.
.
What I'm not understanding is why you suggest getting the official patch even if one has GOTY?

Thanks Psymon, I'll incorporate some of your suggestions.

About updates for tools, etc. If you have multiple clones and you want to update the tools or mods, you will need to update each clone regardless if you have pre-installed them in your clean clone.
So this is really just a matter of choice. Look at it as if the pre-installed stuff is defaults.
The real consideration is if you want those tools or mods to be available in every single clone or not. It's much easier to add what you want after the fact compared trying to remove it.

Regarding INI tweaks and pre running the game to generate the files.
Keep in mind that when copying a clone, mTES4 does not copy the profile or appdata folders. This means that any changes you make to the Oblivion.ini in your clean clone will NOT be copied to any new clones.
To get by this, make your tweaked ini and then copy it to the Oblivion_Default.ini in your clean clone.

My understanding is that the GOTY version (Disc 1) is unpatched.
The latest patch is only applied by installing SI (Disc 2), which is not recommended in the guide.

Agreed which is why I think it better to not add them to the base clone.
Oh yeah forgot - but it is so easy to copy those things over after the new a clone is made and with the work done already all that much faster.
Huh didn't realize that. Well so many mods require SI these days I can't even imagine installing without it. Besides as many have found out installing SI via BAIN is funky - it always shows as red even though it is installed. Same is true of DLC with Fallout3. I still have all DLC in BAIN folders for control, but I think for most GOTY people having SI is part of the base install.

Most of this though is about preference and I think you did a great job outlining most, or all, of the concerns to be aware of - then let the end user decide. They will anyway.

Now with the more controlled removal of clones there is very little risk in using this.