Some more thoughts for the rough plot.
It will require redubbing, some new shots and CG etc. Bery ambitious.

Alot is based on a reinterpretation of Count Dooku as new Vader:
He is a mysterious masked figure, with a distorted menacing voice. He is the leader of the Seperatist Faction. Noone knows his real identity, where he came from etc.?
A new actor with a matching costume could stand in with a mask, and a CG mask grafted onto Christopher Lee's face until the BIG REVEAL later on. The Mask allows for easy re-dubbing, so we can see alot more of this consistent villain now.

ROUGH PLOT SO FAR

Film opens with the conquest of Naboo and Amidala's escape. The entire affair is watched by our new Dooku from the bridge of his Flagship (much like Vader). He contacts a mandalorian via hologram, demanding her assassination.

Cut to a star destroyer passing over a blue planet, a Jedi fighter drops out the bottom. A very editted sequence in Kamino, acts as an introduction for Obi-wan. He encounters Jango Fett (with Zam replacing Boba in Slave 1) and pursues him under instruction from the council. The clones are still commissioned by a long dead Jedi master.

Amidala settles in Coruscant (no bombs). Somehow she needs to discuss the plight of naboo, without using footage from Ep1 to avoid all the makeup. This might be a good opportunity to introduce Palpatine.

Assassination attempt on Padme in her apartment not sure how, but somehow Obi-wan intervenes, diving through her window and the scene continues. Zam shoots out the ball droid thing and Obiwan falls, only to be saved by a new hero - ANAKIN SKYWALKER (super late introduction). Everything follows as normal.

-----

Not sure how to tackle it from here. The lift scene could be used for the Jedi Council meeting, maybe they revisit Padme afterwards. Really not sure how to explain anakin and padme going to naboo, although it could be a new planet. Also the visit to tatooine might also not be as appropriate now.

Ultimately it turns out that Count Dooku is actually *Sifo Dias*, he removes his mask to reveal this at the beginning of the duel, then gets out his lightsaber. It is just obi-wan fighting him, and all the 'Join me obi-wan' dialogue is used during the fight. Anakin jumps in from nowhere like before, maybe having flown in from a different transport.

Probably no 'Dark Side' in this episode, save that for the next one when we might not know if its really that bad or not.

Lend me your brains people!