I've just checked my save files due to large lag spikes in game and have found them to be excessively large. They started at ~40mb and are now upto ~60mb and are, although more slowly, still increasing.

I have tried disabling all mods (and waiting a few days in game), and running the save game cleaner mod - which although did reduce the files a little, it was only by <2mb which I guess means it didn't fix the problem.

Load order (this is fine when tested in BOSS, although I must admit with a lot of 'dirty edits' (of which I'm not sure what that means)):

There's no way to magically clean a save file.

SKSE has a setting to help rein in out of control scripts, but it's not a miracle cure. It only reins in scripts of a particular type.

So any idea what I should do next? Where I should start in resolving the problem?

Get TES5Edit and clean the mods. It's easier than you think. The Read Me for that program has a link to a tutorial that shows you how and why this program works.

The TES5Edit thread is right next to yours on the boards.

I'm doing that as we speak, watching GopherVids Youtube guide. I hope it's safe because Dawnguard has 600+ dirty edits.

If you watch the video that is linked in the readme, you will get some more information. The author and Gopher disagree on some points, and I tend to side with the Author of the program on this one. The most important being to not do all the DLCs at once.

Note, I cleaned my game, following the read me link method, and my game is happy and it purrs along.

Well I only did Dawnguard and the other smaller non-dlc mods that needed cleaning according to BOSS.

Although a lot of the mods/dlc still show up red in the list, iirc that doesn't mean there is a problem. And BOSS now gives no other suggestions other than the Bash Suggestions.

Will this help in anyway to unbloat my save?

Same as CCNA.
As a matter of fact, it has been a long time since I had any problems with Skyrim since I cleaned...

But really, it is so easy to do that once done, you will feel silly for being nervous. I remember being a nervous nelly about touching important game files, so I followed a guide and thought "Okay, apply filter...done...Remove records...done...undelete references...done...wait, that was it? Dang, that was easy!".

Yeah, it's really daunting when you don't know what does what, but it often turns out to be quite a simply process when it comes to modding Skyrim.

Unfortunately, cleaning my mods has not changed the save game issue, and upon loading, waiting and saving the save file has only increased ever still.

I remember someone saying that waiting 30 in-game days helps a bit (It gets rid of things like corpses, and every cave respawns).

I did it once and I didn't really see a difference for me but it is worth a try

No.

Cleaning the DLC is kinda pointless to be honest. People like to throw that around as if it's some magical cure, but it generally doesn't actually do anything. And while cleaning your mods of unnecesary edits is a good idea, it won't prevent bloating like this, nor fix your current save.

What cleaning with TES5Edit does is prevent crashes caused by a mod attempted to do something with a deleted record and prevents dirty edits from screwing up other mods.

These two tools might help in bringing that 60 meg monstrosity of a save down in size.

http://skyrim.nexusmods.com/mods/31724

http://skyrim.nexusmods.com/mods/31675

I've never used them myself, but I've heard positive things about them.

However your main goal should be finding out what caused this. Unlike what you suspected in your OP, SKSE did not cause this.

A possibility is that one of your mods has some broken scripting.

But another point of concern is that I don't see the Unofficial Patches or any other mod that removes stuff like ashpiles and weapons from enemies that fell on the ground. You may want to concider a mod that does that (my advice would e the unofficial patches).

Those should be avoided. There is no way to fully "clean" a save.

There is not much you can do to reduce a Save file size, other than playing a tidy game. But, once the file is large in size, it's going to to stay that way.

Cleaning the DLCs and other mods will just reduce any problems that you may have down the road that can lead to save problems, like corruption of the saves and crashing. Saves played on a cleaned game should not grow as large either. However, there are a few things that lead to save file growth that have nothing to do with the cleanliness of the DLCs. I suggested cleaning the DLCs because you mentioned the dirty edits, and those should not be left in the game, even if your not having problems.

To play a tidy game, you have to clean up after yourself, not change a cell unless you have to (although the game will reset these after 30 days) and not leave any weapons lying around after a battle, things like that. Note, I do not set out to play a tidy game, but my largest save is still less than 15 MB, and this character has done most things in the game.

This didn't work unfortunately.

I've checked and my SKSE is installed perfectly, so I see no reason that it can be that.
If the scripts are broken in one save (the one with the large size), would they be broken in an old save. Say I loaded an old save (around 7mb in size), would the broken script eventually make that increase, or not?

Also, I have both the Skyrim and Dawnguard unofficial patches...

The saves in this game are quite complex, as you are discovering. While the reasons for them corrupting are usually related overwrites or mod issues, or crashes on save, other people saves get weird for no discernible reason. Well, I have some ideas on that, but not for this thread.

If your sure your mod mix is kosher, then load up and earlier save and monitor the growth. I don't know the acceptable rate, by my level 54 almost completed the game character is less than 15 MB. I also don't run very many mods. However it is mod mix stability that is more important, not the number of mods.

Oh, woops. Failed that spot check.

Yes. If there's a broken script (or whatever is causing the bloat), it will continue to be broken if you load your old save or even start a new game with the same modded setup. You need to find and remove the cause of the bloating, or it will just happen again.

I lost a level 87 character once due to save file bloat. It was my fault because I used too many heavy scripting mods and installed/uninstalled without precautions. I learned the hard way...

In my current playtrough I'm already level 83 and my save file is always in between 15-16 MB large. I still use plenty of mods, even the ones that use many scripts but I test them enough before use them permanently and now I monitor my papyrus log and my save file size constantly. I don't use Autosave, and I never rewrite a save file... I always create a new one and delete or move away the old ones to avoid having the saves folder too crowded.

Okay, so I have two theories of what is causing this then. One being that I clicked the uninstall button in the MCM menu for Enhanced Blood textures by accident, without uninstalling it outside of the game, which since then I've had this problem. However it seems that this wouldn't cause that much trouble, and I'm currently waiting out the 30 days with my mods off, and it's still happening.

The other was a problem I had with Dawnguard, in which I loaded an old save with very, very different mods installed inside the dawnguard castle - mid quest. And so everyone attacked me and a lot of strange things happened. Unfortunately in my attempts to control the madness, I left the castle and my game autosaved. This occured the day before I messed with Enhanced Blood textures.

Of course it could be neither of these things, however these are the two stand out occasions in which I really tampered with something I shouldn't have.

Which "savegame cleaner mod" did you mean?
SKSE has a feature to remove orphaned script updates, which can stack and be one reason for bloating the save (ClearInvalidRegistrations); did you try that?

Edit: Uh. Removing mods from a saved game (by whatever means) is a bad idea.
Switching off the mod in the MCM should be fine, though. That's exactly what that option is there for. Whether you uninstall or not, shouldn't matter; it would be better that you switch off the mod in the MCM (if it offers that option) and let it remain in your load list.

http://skyrim.nexusmods.com/mods/31724/? Though it did absolutely no good.

Can you tell me more about this feature of SKSE? I don't know what that is or does, but it sounds like it might help..?

In your Data folder, you have a folder called [SKSE].
Create a text file called "skse.ini" and write the following:

[General]ClearInvalidRegistrations=1

(I'm not sure whether the General heading is needed, but better be safe.)

Play for a while; the command needs some time to remove the stacked script bloat.

Okay, awesome. I'll give this a try and see if anything happens. Any idea roughly how long I need to play before I notice any difference at all?

When the feature was introduced (removing Sounds of Skyrim - Civilizations from a game was a major reason for having bloated games), Arthmoor wrote: "A save I let the Civilizations module go crazy on returned to its original size. Took a couple of hours, but it worked, and no ill effects."
So if it works, you'll see some effects probably earlier, but it needs a while to do all it can.

If that kind of errors is the reason - the command cures one reason only. Good luck.