The Episode II dream has evolved into a rather long and kind of abstract piece of work, so just about anything can fit at this point.
I really like the way you are handling the dreams, and would suggest altering those in RotS to match. It seems MagnoliaFan is doing something similar in his dream, incorporating dialogue from Qui-Gon and Shmi as well. I would edit it just a bit different from you however:
Qui-Gon: It will be a hard life. One without reward. One without remorse. One without regret.
Shmi: Don’t look back. Anakin…
Anakin: Mother…
(Images and sounds of Tuskens attacking (from ANH), and beat up Shmi)
Anakin: No…please, no…mom!
(Cut to the close up of Anakin awakening from his nightmare)
I'd be against intercutting Anakin squirming in bed, as it takes focus away from the dream and just look awkward. The final shot of him opening his eyes at the end would be more effective, IMO.

If you're going to change Mace's blade color, blue is definitely what to make it. I'm sure you'll be a good judge of whether it looks good or not.
Certainly. Dooku doesn’t really have a theme as much as just the 4-note motif from Uranus, and it doesn’t show up often- only once in a while for dramatic effect. For instance, it’s introduced when Dooku enters the interrogation room (where Obi-Wan is held). It is heard again in the arena as Dooku comes out. And finally, as Dooku turns around to face Obi-Wan and Anakin, it is used again.
I quite liked the "Seperatist Theme" used in AotC, very subtle, but effective. The Holst will be a neat alteration though. And I'm glad you decided against using the 2001 motif at the beginning of the duel (too recognizable).
You seem to have thought through everything about Dooku being a Sith, and I do like him and Sidious' final scene. A future RotS change I think is necessary with this would be a sound clip of Christopher Lee saying something along the lines of, "Wait! You don't understand!" Then Anakin cuts his head off.
I have to get III done before I to complete my recording for Anakin. Without III, II is incompatible in SW. Another big picture plan- for Episode I, I am going to use a prologue before the Main Titles. It seems fitting to provide some history before beginning a 6-film saga. So we have the fanfare along with the Fox Logo, Lucasfilm Lmtd., etc. etc. Then, instead of going directly to "A long time ago, in a galaxy far, far away," we go to a new frame of text. "A long time ago, in a galaxy far, far away, there was a great war. The Jedi Knights, guardians of peace and justice..." etc. We have brief shots of battles and spaceships and other things in between the background story. I'll need to do research into the EU for ideas on this.
This is a very intriguing idea, one that certainly merits more in-depth discussion at a later time.
Queen Padme Amidala: I'm not sure how much of this applies to your edit, as what scenes and line have been added/cut. The Four People whose lines would have to be altered would be: Padme, Obi-Wan, Palpatine, and Mace (Anakin is not a problem as you're redubbing him anyway). All 4 of these characters have lines in TPM that can be scavenged for use in SotDS. "Queen," "Your Majesty," and "My Lady," can all serve as substitutes for "Senator." I'll have something more specific later.
At present, I am only committed to sending out 3 copies of this- one to Rikter, one to MTHaslett, and one to Commander Courage. I can't commit to any more, so Rikter will be the distributor (unless MTH or CC make copies as well).