Well, it wasn't always possible to make the jokes work with the actual footage or at leats make them work as well (eg. the scene where Luke imagines what it would be like if they were "father and son.") I could use the FAMILY GUY jokes as a voice-over because they are mostly faithfull to the orig. scenes and only change the dialog, whereas ROBOT CHICKEN often expands on the existing scenes and so the film footage doesn't fit the dialog)
As to what kind of decisions kept material in or out of this Version 1.0... Well mainly I only used the jokes that I really liked (so most of ROBOT CHICKEN but eg. just a few from FAMILY GUY). Then of course I couldn't use anything that contradicted the storyline. I tried to keep the original story understandable from this cut but keep the whole trilogy under two hours which it think I pretty much managed to do.
Don't have time for more right now but I'll get back to you.