I'm having a hard time again using wyre mash to merge my mods. I'm trying to clean my mods before I merge them, since it's a good idea right? It doesn't hurt to clean all the mods you have does it? And here comes another question, should you use wyre mash on your mods? I'm using it to try to clean my saved game so I can use the Passive Wild Animal mod in my current save, organize my load order, and fix some other things that I may have not known were there. I just have no idea what I'm doing... I may have made things worse, like I have no idea what the merged levels, dialog, and objects in my data files does, and don't know if I should check them or not. If I don't check them, then I'll get this message saying Helluva weapons mod cannot be found or something.

A clean mod is a usable mod. Always.

I use Enchanted Editor to clean mine. They smell so pretty when I'm done.

Some mods aren't meant to be cleaned and should say so in the readme. Intentional changes to GMSTs as well as activators may be reported as bad by TEStool. It is wise to read the readmes before cleaning any mod, never use a "just fix it" option, don't merge dialog, and always make backups of your mods and/or keep the original archives.

Also, don't batch clean. Clean one at a time and test. That way, if you've overcleaned a mod, you'll know which one you have to replace. If you clean in batches and only one is corrupted, you won't know which it is. One question, since when does Wrye Mash have a merge function? Have I missed it all these years or is it new?

What about using wrye mash on your mods? Should you always use merge your mods together? I had no idea what I was doing, and don't know if I did a good thing by merging the mods together.

Crap, I did use the just fix it option.

Here's the list of the all the mods I'm using. Can you guys tell me which one's shouldn't be cleaned?

Morrowind Patch v1.6.50BETA
Better Heads
Better Bodies
Abu Manor
passive healthy animal
real signposts
dh_furn, dh_furn_stores, dh_homes, dh_thriftshop
Archmage Tower 2
Nerevarine Castle
Crehange Manor
Better Books
Horror Mod
Akavirian Armor
sg1 -sgaileach_estate1.2.
Cragonmoor v 1.1
DM_DB Armor replacer
Clean Hunters rifle
Better clothes
Ravenloft
H.E.L.L.U.V.A. complete weapons
H.E.L.L.U.V.A. complete armor
Art of War Museum
New Argonian Bodies
New Kajiit Bodies
Animated Morrowind
Particle Arrow Replacer
Psy_VGR_Armour
DreadKnight
Unique Tombs
More Better Clothes
Morrowind Code Patch
Archmage Tower by Antares
Ondurin Vareg
Antares Big Mod

No, it isn't necessary, nor is it even a good idea to merge all your mods on general principle. If you're close to the mod limit (255 was the original limit), then you might consider merging mods that don't change similar things. The only thing you always want to merge are Leveled Lists and Wrye Mash has a very good method for that. Sorry I didn't get my advice to you sooner, but as long as you have a backup of your .esps if you've overcleaned, it's fixable without too much trouble.

Never, Never, Never use the "Just fix it" option. It just causes problems.

TESTool really only works for only two things.
- Cleaning an esp of junk data.
- Merging Objects

Like Elaura says, don't merge esps unless necessary, and you exactly what you're doing.... Sounds like you're new to mods, so do not attempt merging yet.

But you do want to create a Merge Object.esp
And with Wrye Mash, you'll want to create a Mashed List.esp
These two esps will ensure that different mods work together in two ways:
- Different mods that affect the same object will both be recognized
- Your Leveled Lists will be accurate (very important to play a balanced game)

And yes, Wrye Mash is the essential tool if want a clean/healthy modded game when using mods. Learn to use it It is so very helpful and awesome.

When you have all your mods, and your MergeObject.esp and your MashedList.esp, run http://code.google.com/p/mlox/wiki/Mlox for even more advice and organization.