Yes. All hope is not lost. In the meantime glad to hear the informal version has been of some help to some people.
I'm adding in a to-do list cribbed from a thread about reinstalling MW, Tribunal, BM and mods afresh based on http://www.elderscrolls.com/forums/index.php?showtopic=382512 containing advice from manooly and other mod users and makers, along with some heavy edits from bjam plus a few small edits of my own. When WryeMash is needed, it appears in BOLD:
1 - Unistall the existing game/MODs
2- Reinstall Morrowind, Tribunal and Bloodmoon
3 - Install Better Bodies / Better Heads
4 - Install face replacers (changingfacesnpcreplacerupdate.7z, and add-on)
5- Install all of texture replacers MODs (Ultimate Textures-Complete, flask replacers, silverware replacer, weapons,armor replacers, clothing/robe replacers, illuminated windows, book jackets, etc.)
6 - Install clothing replacers (better clothes, Ultimate_Textures_-_Clothing.7z)
7 - Install the larger MODs (Morrowind Comes Alive, Sound enhancers)
8 - Install Official plugins
9 - Install new quests - (White Wolf, AndromacheInstaller.zip, etc)
10 - Install extras (barabusfireplaces2.zip, bobs_armory.rar, carnithusarmamentariumcomplete.zip, horseranch31full.rar, marksmanmodversion1_45.rar, etc.)
11 - Install playable faces
12 - Check for conflict between mods with TESPCD
13 - a - Lauch Wrye Mash and synchronize the mod with the master files
b - or update header with Tes Tool
14 - use TESTool, TESAME, or the Enchanted Editor to clean mods of GMSTs and dirty references; a link to the list of mods that perhaps should not be cleaned with TesTool appears at the beginning of this thread (read to end of thread and/or take with grain of salt)
15 - if this has not yet been done, check mods to be played via TesTool, Wrye Mash , TESTool, [MWDatafiles screen, or TESCS?]
16 - arrange load order using "reorderPlugins.zip", reOrder Mods [ck name??? I have a mental block here!], TESTool, or Wrye Mash
17 - a - Run TESTool to merge levelled lists and objects (not dialogue, as it, unfortunately, usually breaks more things than it repairs), or
b - Run TESTool to merge objects and then merge your Leveled lists with Wrye Mash
18 - Lauch Wrye Mash and (if not already done in step 16 or 17) Lock Times -> It will be very useful if you decide to add / remove some mods later in your game;
19 - Run Morrowind FPS Optimizer.v1.96.zip in background
20 - Start new game.
This could probably use some more tweaking, but perhaps it will be more helpful than the outline in the second post for some users.