I know that you guys have set a lot of things up for these edits, and I'm glad that you're going to have an outline and "script" posted online to refer to as you work.
---Replacing Sidious with Dooku? A bit of a stretch. I do like the idea of Qui-Gon talking to him from Tatooine though, to establish the relationship between them. If it helps, there are tutorials online for using After Effects on how to generate holograms and insert them into existing footage. This method could allow you to create the footage you want of Dooku leaving the Order, if he is a hologram in the center of the Council Chamber. Just a thought.
---Cutting down on Gungans? I'd have to agree with MTH (believe it or not!) that the big battle sequence, minus Jar Jar's antics are a must for Ep I. Cutting down on the Gungans too much, no matter how annoying they may seem, may leave you with more holes than before. Subs or dubs can be used to make them tolerable, as you've said. We do have to make sure that any dialogue changes can be balanced by what other characters will be saying though.
---Grievous=Maul? I'm all for this one. I personally don't believe we need to see any kind of transformation in Ep II, especially if there's a chance that Vader's transformation will be shown in Ep III. That would answer any questions abotu how this was possible. Leave it a surprise, a new reveal for a new saga. You can use the new dialogue of Grievous in Ep III to drop clues as to his true identity. For example on the bridge of the starship (change in bold), "Ah General Kenobi, The Negotiator. We meet again at long last." Leaving that hanging might go overlooked by the Jedi and most viewers, but if Obi-Wan and Anakin are concentrating on the matter at hand, this would go unnoticed in the moment. Then, when Obi-Wan finally has the big one-on-one with Grievous, you can leave him dropping more clues in the initial saber fight until the reveal comes just before Obi-Wan defeats him. There is some symmetry to the battles of Ep I and Ep III then. Obi-Wan is older and wiser and has allowed himself to grieve for Qui-Gon by this point. No sense in having any concerns of him being overly emotional.
---Dubbing via alternate languages? This could get sticky. I mentioned this with my roommate over the weekend and he had a comment. This could be bad since you're releasing it for the whole world to see. For example, I believe someone mentioned German as a source for some characters at one point. So what happens when someone who IS German watches the movie? See what I mean? He actually recommended that we get someone who speaks a completely foreign language to write everything. who Subtitles btw are very easy if you're burning them directly into the footage. Use the "titles" track/tools from Womble to add what you need, where you need it. I used it for my first "test" DVD project.
---The Montage at the start? Ick. Just doesn't fit.
Just a few thoughts there. I do like the ideas I'm seeing though, and I'm looking forward to seeing how it all turns out.
EDIT: Didn't see the outline, as I started typing before it was posted. Looks good though.