Can I install this thing while I have fcom super pack installed? Also, how far allong is it? Last time I tried it it had lots of missing meshes and stuff. Probly my fault, really... crashed alot too.
If I have to have to just have vanilla oblivion... can I install a seperate folder and install a vanilla version of oblivion, like have it on my hard drive twice? Cause I would just to be able to play this.

I believe the fcom question
I believe the fcom question is answered in the download / release section (if this does, in fact, answer it, I don't use fcom so I don't know):
"Morroblivion happens in a different worldspace than Oblivion, so where Morroblivion mods appear in the list really does not matter except possibly with COBL. I use COBL as part of an FCOM installation, so I personally cannot give advice on where it should be if used separately; for that I can just tell you to read the documentation carefully."
Check it out here: http://morroblivion.com/forums/morroblivion/mods/753
As far as how far along, I just finished the main quest, without seeing a missing mesh that I wasn't responsible for myself. I don't believe any messes are missing, and as you can see at the link, all of the non-expansion quests should be done.
You could definatly duplicate your folder; I did that with Nehrim. Make sure whichever folder that you install morroblivion on is not under program folders: (I put mine in a 'games' folder). THough I play morroblivion from my normal oblivion folder, so I can keep my good character and use him for the morrowind story.
I would suggest you read through the relsease topic (the link I put up above). THat should answer all these questions for you. ;)
Hoped that helped.