Nice work on those TPM openings, guys. Personally I wouldn't change that much, since I think it's the best part of the movie. Some good action and a very fitting introduction of two (main) characters and the Jedi themselves.

I have some suggestions for this scene, if you don't mind:

It never bothered me that Gunray contacted Sidious based on TC14 guessing Qui-Gon and Obi-Wan were Jedi, but you seem hellbent on changing that, which is fine :P. The cobbled together line by Gunray is very effective, but might it not also work to just change TC14's line into something like "I verified the ambassadors identity and they are Jedi Knights"? It seems very reasonable to me that a protocol droid would know how to recognize a Jedi. Also, a droid is easy to overdub, and it would explain why the droid is still in the scene.

This is a great new introduction for the Jedi: we don't see their faces until they blaze onto the screen in all their ass kicking glory. But I don't think there is enough introduction for the guys of the Trade Federation. Cutting into the middle of a scene, where one of them stands with his back at the camera, isn't a very good introduction for the main 'villains'.