I want to be able to have all factions/quests pertaining to them completed and being the "leader" of each and being recognized as such.

A bit asking but I know you guys can help me out!

Adding and removing from factions is as follows(I don't recall if the 1 at the end is required for both).

addtofaction xxxxx 1
removefromfaction xxxxx

I've had mixed success with it, but haven't played around with it that long.