Since you guys are starting with Episode 1, I'd recommend figuring out the major changes that need to be made for all six films before actual work is started. That way, you guys don't paint yourselves in a corner later on.
And while we are on the subject of ghosts, (here's where I get stoned for heresy), Alec Guinness might have to go. A guess it depends whether Shaw or Christensen is going to be used. I would not mind Christensen as much if he were next to Mcgreggor. Actually, even if you guys don't use it, it would be neat to see 'prequel version' of this scene with Hayden, Neeson and Ewan (not necessarily to put into the movie, but maybe to have as an 'Alternate scene' for a Bonus Material disc). Anyway, we need either only the old actors or the new actors. Not both at the same time.
If Quigon is in this version, then Luke would need to know who he is so his appearence makes sense. This seems like a good reason to replace Ben's mention on Dagobah that Yoda trained him to Quigon trained him.