This sounds like a very interesting project. There's nothing I can offer in terms of modding, but I have some ideas I think would be fun:
HK-47 mentions in KotOR I that he used to kill political opponents for his master, and maybe you could take up something similar. Work out who to join to make the most credits, and influence the outcome of whatever political battle is taking place. Similar to Onderon, you could have news terminals talking about the events you took part in.
There would be very mixed reactions to there being a Jedi back on Coruscant; and seeing as the reward for capturing a Jedi is apparently enough to afford a planet, it wouldn't be a safe place for the Exile and his/her companions.
Getting in to the Jedi Temple should be saved for last, maybe it could be under some kind of lockdown and by helping the right politician, they can find a way to get you in there. The plot with the Senate/politicians would really just be leading up to the main event: the Jedi Temple. There's not too many options for an original "boss" fight at the end of the Temple. Maybe instead of a standard fight there could be some kind of mystery to solve or item to find. KotOR II has always been more dialogue-centred than the first game. Obviously there'd be enemies in and around the place. One idea I had was that you can find a Force Ghost of an old Jedi Master whose apprentice went missing in some sort of accident or battle, and couldn't rest until they were sure of the apprentice's safety. You could examine Temple records and get information from datapads in corpses to determine the fate of the apprentice and other Jedi in the temple. You'd end up finding evidence that the apprentice survived the incident that killed the Master and return it to him. The Dark Side option would be to tamper with or destroy the evidence and leave the Master either thinking his apprentice was dead or that there is no evidence, leaving him to suffer as a restless spirit forever.
It'd be a fun adventure and getting around the temple could make use of various skills and party members. Also KotOR II lacks some good puzzles (which aren't given away by having high intelligence) so it would be an ideal place to put some in. I don't know if what I'm asking for is possible, but I thought I'd share my ideas.