I had completely forgotten about the fact that Jar Jar gets banished. It does indeed flow better in your version.
I had actually forgotten the pod race deleted scene when I wrote this, I was talking more about the one right before it. The one during the race with the repair droids I actually really enjoyed.
For Ani's race record I honestly never had a problem with him never winning before. For me the bigger issue (which you solved) was his immature, childish behavior. I mean he's still very young and presumably he's only just started racing so it's plausible he did just a few races before and failed, crashed, Sebulba tricked him... but he's learning. And Qui-Gon gives him the guidance and advice he needed to push the Force in his favor and win. To me it's very similar to Obi-Wan guiding Luke to drop the bomb in Ep IV. And in that case I always kinda felt "It's not that hard I used to bullseye womp rat and they're not much bigger than X" was just a cheap and easy way to establish Luke's ability. I mean he's surrounded by veterans in that room and it makes them look like incapable people and this new brat comes along and says "nah you all suck, it's not that hard". Anyway segway over!
I hadn't realized you had already removed a shot from that Maul bit. I think removing those 2 extra would only shave 1-3secs but I understand it's a slippery slope and flow continuity is important.
Speaking of, it reminds me of a scene where the cut is a bit abrupt (probably the only time I felt a cut that you made). It's when Ani and Padme are in the ship and Ani says that he's cold. Padme talks about her worries for her People and then very abruptly says "you miss your mother". I assume it's because you cut the whole "I made this for you" bit and it can't be salvaged but the cut and change of subject is noticeable. I think you'd be better served with just cutting that line altogether. We can see both are worried and it's implied if not obvious that he's sad because he just left his mom.
And finally for the Viceroy hostage. I guess one way to fix it would be to cut the Ani bits before the Queen take the Viceroy hostage but that's some major change and I'm not sure it's needed honestly. I always saw those 3 paths in the ending climax as happening at the same time, just obviously they can't be shown at the same time. It's not impossible that the Queen does her trick around the same time Anakin is crashed in the base and shooting, they just both have to go through with the plan on their end in case the other one fails.
Totally understand about the end credits :)