It's been over a year since I've played Morrowind on the PC, so I pretty much forgot a bunch of things about wyre bash and installing mods, knowing which mods conflict with each other and which mods needs to be loaded after others. So I wouldn't mind if someone refreshed me on that.

How do I clean mods, and which tool is the best way to clean a mod? I've cleaned mods before with a certain program called tescleaner or something, but how do I know if a mod shouldn't be clean or not? And I never actually did get the hang of merging certain mods together. How do I know which mods needs combining as well? I don't think I ever successfully merged mods together before.

https://code.google.com/p/mlox/downloads/list

It's fairly simple to use but the instructions are more complicated then what's actually involved.

http://www.fliggerty.com/phpBB3/viewtopic.php?f=9&t=5734

Yeah, I think that's what I used before. Now how do I merge leveled lists?

You'll want to make a MashedLists.esp with Wrye Mash.
First, I recommened this version. Easiest to install: http://www.gamesas.com/topic/1106095-wrye-mash-stand-alone/

The documentation is from an older version, but all the steps are basically the same. http://wryemusings.com/Wrye%20Mash.html
http://wryemusings.com/Wrye%20Mash.html#MergingLeveledLists (very easy)

TESTool is still good for 2 things.
Cleaning out the bad GMSTs on an mod, and making a MergedObject.esp (avoid using TESTool for anything else)
And there are other tools that can clean GMSTs.

I think I actually wanna merge objects instead of lists. I may have gotten them confuse. Merging list is where you end up having a mashed list right? If so, then I already know how to do that. What I don't know is how to merge objects, like when two mods affect a merchant's inventory and you wanna see both of the items provided by the mod in the merchant's inventory list.