Further to my previous comments it might sell the idea of the Federation having a prior claim to the Gungan homeworld if you (or someone who may assist you) altered the statues at the Gungan sacred space to look like the Neimodians.
Perhaps someone like Bob Garcia (who has helped others with their edits in the past) could give you a hand with this if you are not able to do this yourself.
Similarly The Cutter might be able to assist you with ironing out the problematic music breaks.
It might be possible to remove See-Throughpio from the pod race celebrations as well (he could stay as the flag holder as he could be taken for just a random droid).
It might help to further trim Anakin's approach to the Federation ship as the shot makes the ship look rather small (when it's meant to be a threat) and the line about the auto pilot taking them there sounds more like something Ric would say than genuine dialogue.
The line about switching the auto pilot off gives us the necessary information but sounds like real dialogue.
As you have taken the shield gate closing on Maul and Qui-Gon away (which creates a few continuity errors which you may get help with) you could experiment with swapping the current shots of Maul behind the shield at that point with some of the more mocking and menacing ones of him staring down the kneeling Qui-Gon.
It might also make Jar-Jar seem more proactive if you added a line about Jar-Jar having an idea while hanging onto the bomb cart (making out that he released them deliberately).
You still get the comedy of him trying to dodge them but that plays like Han charging at the stormies in ANH and then having to run away again later.
It's a good edit but by improving the picture quality (the DVD colours are really ugly perhaps an adjustment would give your edit added vibrancy) and ironing out some of the rougher edges it could be so much more and it's definitely worth the extra effort.
Well done for getting this far so quickly (i know it can not have been easy) and thank-you for sharing it with us.