Originally I thought that my game freeze/CTDs were caused by "Faulting application morrowind.exe, version 1.6.0.1820, faulting module mwse.dll, version 0.9.4.0" had to do with MWSE. But, a week ago I got a 'light bulb' and looked at my Warnings and every time, without fail, I got:
Not able to find Ankle part in BC_extravagant_pants_02_Ma.
Not able to find Knee part in BC_extravagant_pants_02_Mk.
Not able to find Upper Leg part in BC_extravagant_pants_02_Ml.
I installed Better Clothes v1.1.exe several times and nothing seemed out of place in CS so, I had to uninstall this mod. The CTDs which plagued me for months stopped. I also got freeze up with Clothiers of Vvardenfell v1.1.exe "Not able to find Foot part in KO_Black_f_boot_f." Has anyone one else had this problem with these clothes mods? What causes the game to not find parts that are clearly seen in CS? Are there files still missing in these mods? Are there patches or can some patches be made to fix this? Are there alternative clothes mods? Are there 'How to CS fix' Youtubes? I would like to have these mods back, the vanilla 'Barby and Ken' dolls are terrible and restarting the game every twelve minutes really svcks. Thankyou

Any warning like "Not able to find body part... etc" are harmless and can be ignored. They have nothing to do with your crashes.

You are not missing any files or body parts. The BB body parts were not originally used in the game, so the game is confused to why they are there... but they cause no problems at all.

It's hard to ignore this when the screen is completely frozen and the only way to get out of the game is to restart the computer. Is it possible that when an NPC that is glitched by these missing clothes would also freeze the cell transition?

Anything is possible, but Better Clothes has been out for a very long time and everyone who run it gets those same errors. They do *not* cause freezing or CTDs. If you wish to test this, take out better clothes and try again. In the meantime, it would be helpful if you posted your entire Warnings.txt file as well as your mod list in load order.

Based on this:I'd guess your CTD problems are MWSE-related.

What version of MWSE do you have 0.9.4a (I guess)? Might be related to Data Execution Protection (DEP), is that enabled for all applications?

What happens if you start a new game with no mods loaded, but with MWSE active? Do you still get CTDs? What happens if you disable MWSE and start a new game (again with no mods)?

If both of those tests mean no CTDs then I guess it's one of your mods. Hmmm, might be worth looking at those first: Post your modlist and warnings.txt as Elaura describes.

I did take out Better Clothes and the freezing stopped. I reinstalled the game from scratch with Better Clothes 1.1 last [saved in CS]. The game worked perfectly [90+ mods WITHOUT one single warning that is, NO MOD CONFLICTS] for four straight hours WITHOUT A CTD [48 fps]. As I attempted to leave the Mage Guild [see the vary long list http://www.gamesas.com/index.php?/topic/1190499-searching-for-clothiers-of-vvardenfell-v11/] and now I can't leave any of the Mage Guilds without this screen freeze and it is the Better Clothes mod ONLY that coincidently and exclusively shows up in Warning. The music still plays but that's it. Also, in that link I suggested an idea that could solve the vanilla clothes with a patch that unequips all NPC clothes and a Better Bodies that expands the underwear into a simple eight race+ full body spandex-like garment [I assume the unsegmented underwear is painted on] or colorful body patterns. If you of such skill modders can do this please pass this idea along. Thank You

Well, if taking out Better Clothes worked for you then that's great. I'm sure if anyone wants to see NPCs in spandex bodysuits, then someone will make that mod. Anyway, enjoy your game.