Many thanks to Kingpix for this compilation! In his absence I am continuing this thread and adding a new bugfix at the end (#14 "Who is there? Goodbye" fix to Better Cloths).

http://www.ornitocopter.net/v3-0-release/

See the temporary fixes for known issues at the last part of this post! An official update is WIP.

Thread History:
http://www.gamesas.com/topic/1504990-relz-morrowind-overhaul-sounds-graphics-30-thread-5/
http://www.gamesas.com/topic/1476401-relz-morrowind-overhaul-sounds-graphics-30-thread-4/
http://www.gamesas.com/topic/1446220-relz-morrowind-overhaul-sounds-graphics-30-by-kingpix-thread-3/
http://www.gamesas.com/topic/1419785-relz-morrowind-overhaul-sounds-graphics-30-by-kingpix-thread-2/
http://www.gamesas.com/topic/1414019-relz-morrowind-overhaul-sounds-graphics-30/

Downloads:

• http://morrowind.nexusmods.com/mods/36945
• http://mw.modhistory.com/download--12231
• http://www.moddb.com/mods/morrowind-overhaul-sounds-graphics
• http://www.gamesdot.org/download/Morrowind-Overhaul-3.0-Download-4926.html
• http://www.gamershell.com/download_94205.shtml#mirrorselection
• http://www.ausgamers.com/files/details/html/69080
• http://www.atomicgamer.com/files/100435/morrowind-overhaul-v3-0-mod

Useful Links:
http://www.youtube.com/watch?v=CuOeWG4BXLI (thanks to Weirdsixy of OpenMW)
http://www.facebook.com/Ornitocopter
https://twitter.com/MrMWOverhaul
http://www.ornitocopter.net/mo_wiki/index.php?title=FAQs

Patches and fixes for known issues:
All of these issues and their solutions have been gleaned from the preceding three threads. Credit for them goes to the individuals who originally posted them. I have just assembled the info into a mini FAQ. - Spirithawke

Also of note, users of MGSO might like to know that MGE XE, Morrowind Code Patch, and the MPP have new versions out since MGSO v3.0 was released.
http://morrowind.nexusmods.com/mods/26348. You must install over an existing XE 0.9.9 installation. Please http://www.gamesas.com/topic/1461152-shelter-from-magnus-blaze-13-mge-xe/page-4#entry22758273 before installing.
http://download.fliggerty.com/download--139
http://www.gamesas.com/topic/1474127-mpp-problems-mistakes-and-suggestions/#entry23026512 Look in the spoiler for link & info
http://www.gamesas.com/topic/1480237-bug-in-the-mpp-165d-beta/page-3#entry23722193 Look in the spoiler tab

#1 My custom files (esps, meshes, icons, textures) get overwritten when I re-run the MGSO options.
You can fix this by going into the Morrowind\MGSOO\Options\ folder, search for the files you would like not to be overwritten, and replace them with yours (the ones you want to use all the time).
Note: You should re-run MLOX after running the options to re-set your load order back to what MLOX recommends.
Note2: This issue may also affect things such as MGE / MGE XE, MCP versions installed.

#2 http://download.fliggerty.com/download-13-726 by john.moonsugar.
*Fixes the scroll for summoning Golden Saints in PSsorticon.esp (Option for Magic Sorting Icons) as that plugin accidentally removed the summoning enchantment from the scroll.
A SPECIAL NOTE ABOUT THIS PLUGIN: There are a couple changes made by this mod that are not mentioned, for details on those, and for a copy that do not have those changes, http://mw.modhistory.com/download--12174.
*Replaces mesh Meshes\f\Furn_De_Table_03.NIF so you stop seeing that error marker all over the place where the table is missing.
*"Poorly Placed Object Fix 1.2.esm" was edited to replace French cell names with English cell names. Mostly affecting door destinations.
*"OTR_Coast_Variety.esp" was edited to replace French cell name with English cell name.
*Two optional meshes for glass boots were edited to correct a texture path name.
SEE PATCH README FOR SPECIFICS OF THESE ISSUES.
If you have already started your game before adding this patch and need to fix said save game for removing non-teleporting doors (which any of those the player has already encountered won't be fixed by the patch due to being saved into the player's save game), please see http://www.gamesas.com/topic/1419785-relz-morrowind-overhaul-sounds-graphics-30-by-kingpix-thread-2/#entry21715492 for using Tes3cmd to do this. Alternatively, you can also use Wrye Mash to fix this issue, please see http://www.gamesas.com/topic/1476401-relz-morrowind-overhaul-sounds-graphics-30-thread-4/#entry23085709.

#3 http://download.fliggerty.com/download--852
*Corrects which meshes get used for the male daedric curiass & guantlets as some esps in the compilation do not agree with each other.
*Corrects a texture path in a_daedric_cuirass_f.nif so females no longer have glowing white briasts.

#4 Have there been any reports of empty chests in Bloodmoon? I'm on Solstheim, and every chest I open is empty. This is a major issue for advancing the MQ of Bloodmoon. Haven't encountered it anywhere other than Solstheim.
The empty locked chests in Solstheim seem to be caused by an old version of the "MW Containers Animated.esp" plugin.
Grab the http://download.fliggerty.com/download--687 of that mod (v1.2) from this link, and install it.
(You'll need to replace the Data Files\MW Containers Animated.esp with the one from the archive, and also extract the contents of the meshes folder from v1.2 into your Data Files\Meshes folder)
NOTE: This version of Morrowind Containers Animated requires http://download.fliggerty.com/download--139 for the "animated containers crash fix" and "mod removal fixes" in bug fixes section.
UPDATE: qqqbbb has now posted a simpler set of upgrade instructions than the http://www.gamesas.com/topic/1410102-rel-morrowind-containers-animated/page-7#entry23260558, on each mod download page (GHF & Nexus).

#5a When I try to repair a save in Wyre Mash, it says it can't, because "Better Weapons and Armor.esp" has bad refs. What's that and how can it be fixed?
#5b Has anyone else encountered this error? It is seems to be coming from MGSO, since that is where I got Better Weapons and Armor.
Object reference "azura's servant" missing in master file.
Current file "Better Weapons and Armor.esp"
Cell "Tel Vos, Northeastern Tower"
In Wrye Mash, tab over to "Mods", right click the offending mod, and then click repair refs.

#6 I can't seem to turn off the FPS counter in the top left. I ran the program to change the configuration but the FPS seems enabled regardless if the box is clicked or not.
There are TWO frame rate counters switchable in MGE, one is MGE's, another one is vanilla Morrowind's.
One of them is "Graphic" tab as Display FPS, second one is on "In-Game" tab as Show fps.

#7 Not entirely sure if it's MGSO related, but does anyone else get a really slow mouse sensitivity in the main and character menus?
Morrowind loves doing that, especially when used with any type of mod that might have impact on FPS.
The http://mw.modhistory.com/download--14566 has a great function called "Accelerate Mouse pointer in menus" and it does wonders to make the cursor feel normal again.
And yes, it works with MGE and all other programs. Just leave it open behind Morrowind and it will do its thing. (do not launch MW from it).

#8 Solstheim, Lair of the Udyrfrykte being inaccessible is caused by the replacement for the surrounding ice exit mesh - Data Files\Meshes\x\bm_ex_ice_exit04.nif
Presumably, the entrance hole in the replacement mesh isn't as deep as in the original.
Deleting that file is a quick fix for the issue.
Spirithawke Note: This mesh is used in 3 places, the other two places, which have related doors also, may be inaccessible as well.

#9 Has there been a patch made for the odd naming on some containers found in the included version of windows glow? It's from the "Windows Glow - Raven Rock Eng" plugin. "com_chest_01_pos" was changed for some reason by this mod, instead of being named "chest" it has an odd string of characters as a name instead. I've fixed it in my copy already, but a "official" fix would be nice too.
That odd string of characters is leftover from the Russian version (the author is Russian I believe). No official fix yet, but it is simple to fix in the CS.
Note1: Abot has an Windows Glow - Raven Rock patch http://mw.modhistory.com/download--14155 that appears to fix every other Raven Rock issue EXCEPT the name of that chest.
Note2: That chest actually appears to be a dirty entry. I ran across one in a temple on the mainland I think it was...needs to have a new entry created, and the reference replaced (maybe..needs more anolysis).
Note3: Abot updated his patch, get it from his http://abitoftaste.altervista.org/morrowind/index.php?option=downloads&Itemid=50&task=info&id=45&-Windows-Glow-Raven-Rock-English-Patch.

#10 MGSOO\Options\G_MC\Data Files\GrassVurt's Groundcover - The Ashlands.esp needs to be rebuilt. The esp is loaded with IDs of UNKNOWN_GRASS
No fix currently

#11 Animated Morrowind combined esp has issues which need fixing, http://www.gamesas.com/topic/1475889-oddly-named-books-in-animated-morrowind-mgso/#entry23084031.

#12 Poorly Placed Object Fix 1.2.esm has issues which need fixing, http://www.gamesas.com/topic/1478059-ex-drystonewall-c-01/#entry23122307 for description of the problem and some patch files. A better UV nif for one wall tile is also available there.

#13 I keep running into lanterns!
MGSO 3.0 uses an old version of the Dunmer Lanterns Replacer that accidentally added collision to lanterns where there's not supposed to be any. You need to upgrade the http://download.fliggerty.com/download--690 to version 9.0.

#14 Better Clothes needs fixing to stop the "Who is there? Goodbye" bug. This is caused by a dialog ID that has "Who is there" as a subrecord. Instructions for fixing it yourself with Enhanced Editor are behind the spoiler tag, but the easiest solution is to replace "Better Clothes_v1.1.esp" with the file found http://forums.sovngarde.se/forum/viewtopic.php?p=15#p15.

Spoiler

From a post by Leonardo: All you need to do is load Better Clothes_v1.1.esp in EE and look for the dialogue/dialogue responses group then go through all responses and check if a dialogue ID has the "Who is there?" ID as a subrecord usually at the end to the right.

I found this ID: 1215227585220936854 in the Better Clothes_v1.1.esp in EE. Just backup the esp then delete that ID in EE and save the plugin when exiting EE. That should fix this "Who is there?" issue in-game.

If not then you need to repeat these steps to fix it yourself.

1. Backup the plugin and load the esm/esp in EE
2. Open the dialogue/dialogue responses group
3. Check every entry there is for the "Who is there?" ID as a subrecord
4. Delete the ID in the dialogue/dialogue responses group that has the "Who is there?" ID as a subrecord
5. Save the changes in the esm/esp when exiting EE


Only do this if you know what you're doing and be advised that this could damage your game.

So, I started a new character with my MSGO installation last week, and noticed some added sounds that I felt were out of place, including various people yelling in cities, dogs barking in cities, cats screeching in cities and various people yelling in taverns, including an obnoxious drunk yelling "I once knew a girl from Baldur's Gate." Most of these were added as ambiance, but I did not like the ambiance they created. There are no dogs and cats in Morrowind, at least none that you see, so the dogs and cats making noise in cities kind of grated on my nerves and the disembodied voices seemed particularly out of place since they sounded nothing like any of the in game voices and were just shouting random things often at inappropriate times.

Turns out to be an easy solution to remove these unwanted sound affects. Just go into the Morrowind sound folder where the sounds are listed and replace them with a silent .wav file. I made a silent .wav file that is four seconds long and is fairly low bit rate and mono so it wouldn't unduly add to the size of the folder when used multiple times. Then I went through the sound folder and listened to all the sound files. Whenever I found a sound file I did not like, I replaced it with the silent sound file by simply deleting the offending sound file as and replacing it with the silent sound file that I renamed to match the file I deleted. That way, whenever the game tries to play the sound file with the obnoxious yelling, it will instead play a silent sound file that won't be heard in your game. I play tested for a few hours last night and it worked great. No more obnoxious yelling from disembodied voices.

Thought I would post in case anyone else wants an easy solution to removing unwanted sounds. Another option might be to use Morrowind Acoustic Overhaul, which apparently is now compatible with MSGO. I have never used MAO, so if anyone has any experience using it with MGSO, I'd like to hear how it went.

I wondered a few times where these soulds come from. So they are not tied to any specific plugin file and they just replace some vanilla ambient sounds?

I believe they are tied to a plugin but I am not exactly sure which one. But I have heard the same exact sounds in modded Oblivion. Sounds of Cyrodiil by Cliffworms adds some of the same sounds to Oblivion, even the same drunk yelling "I once knew a girl from Baldur's Gate". Cliffworms Oblivion mod includes a silent .wav sound file and instructions for how to replace the sound files with a silent one if you want to get rid of some of the sounds. That's what gave me the idea to do the same thing in Morrowind. I used the silent .wav file Cliffworms provided with his Oblivion mod but ran it through a converter to make the file size smaller by converting it to mono and reducing the bitrate, bringing it more in line with the file size and bitrate of the Morrowind sounds I was replacing.

I don't know which MGSO plugin adds these sounds, but I suspect there must be an .esp file associated with them. If they were just straight replacements to the vanilla sounds, then you could just delete them and the game engine would just revert to the sound files in the Morrowind bsa. But if they are in addition to vanilla sounds and there is an esp file that uses these sound files, then you need to replace them with a silent sound file because deleting them might cause a CTD when the esp calls for the sound file and cannot find it. At least that is how it works in Oblivion withwith Sounds of Cyrodiil, so I would assume something similar is happening with MGSO in Morrowind.

If you're not sure which mod has the ambient sounds then load your loadorder into TESPCD and search for something that's unique for that sound e.g ID in CS, sound file(s), even a script can be found etc.

Bingo! That's it. That explains why the sound files I found were in a folder called sounds/_ase_. I wondered what the _ase_ was. Mystery solved. Just downloaded ASE and it does add these sounds and also includes this in the readme: