Yes, Morrowind is very different from the other games and below have I listed a few things you need to remember.
1. Do not expect mods to be cleaned from dirty edits, unless the author stated otherwise in the readme and remember to read the readme before installing any mod (I know most people doesn't read the readme, including myself, well sometimes I do read)
2. Morrowind doesn't have FormID as a record structure as both Oblivion and Skyrim has
3. Don't worry about cleaning your gamesave in http://www.gamesas.com/topic/1601492-wrye-mash-thread-7/, it is safe to do that, which is essential to use along with http://www.gamesas.com/topic/1509142-relz-mlox-anolyze-and-sort-your-load-order/ (have the same purpose as BOSS or LOOT) and http://mw.modhistory.com/download-95-7040 (excellent for detecting mod conflicts or other issues)
4. You also need to learn a few, but useful console commands, and one that's often used when NPC's is blocking your path e.g in small spaces like the Mage's Guild in Balmora is ra and the other one is ori when troubleshooting a mod issue
- open the console and type ra (Reset Actor in a cell) in any cell, if a NPC is falling off a cliff or something usually the NPC that runs the siltstrider in Ald'ruhn and Maar Gan
- open the console and click on any object in-game then type ori (very useful when you need to know what happen just before you got a CTD)
Remember, you can always start a new thread in this http://www.gamesas.com/forum/12-morrowind-mods/ and ask for help, if you ran into a mod issue in-game.