It may be possible to pull off there were some nice mock-ups of Dooku standing on a hill looking down at the cremation from a distance.

Having him appear as a hologram during the council meeting may also be doable.

I had the notion that Palpatine had organised events like the Naboo invasion all around the galaxy and the people duped into performing them would end up being the original Separatists (because nobody in the Republic trusted them any more).

So he could be off world when the bulk of what happening in Episode One goes on investigating other disturbances only to come back and find his former student slain because the council wouldn't mount a proper investigation.

As for the coda all you'd need is a shot of a bacta tank in a lab and a reveal to the torso bubbling away (Resident Evil style).

When we see Kamino in Episode Two we know where it was but don't know the connection.

Blacking out the face in Palpatine's cape would create the impression that maybe Dooku was the other Sith (you could even make it so Maul and Sidious are never refered to by name or seen together at the same time so he could even be seen as the Master) taking the heat of Palpatine for the first time viewer (Lucas really screwed up there).