I'd suggest just canning the entire Sifo-Dias sublot, it's too stupid to make sense. The whole mystery element doesn't work, as the Jedi Council say they will devote all their resources to find out who created the army, and then it is never mentioned again. You could start AotC with Obi-Wan going to inspect the Republic's new army.

With regards the Phantom Menace, could you move TC14, and the shot with the Jedi lounge to just after they arrive at the Jedi Temple? The only thing that would need changing would be the windows... Could you just replace the space views in the windows with Coruscant city scape?

Out of interest did you have any pans to introduce Anakin any earlier? As he is the closest discernible thing to a lead character, but doesn't appear for the first 40 mins of the fillm.