Since you’re making a final v4.3 and you’ve already willing to implement last minute alterations (such as the necklace scene), here are some minor suggestions based on other edits:

cut Anakin’s interjection “What are we gonna do about it!” and Qui-Gon’s response (L8 edit);
readd “the entire planet is one big city” line (it creates a slight jarring audio cut and I actually don’t mind this line);
when Qui-Gonn says “The situation has become much more complicated.” I think you should try to keep the shot of Anakin looking back at him if possible;
trims to remove Boss Nass’s blubbering and awkward vocalizations (Octoroxx edit);
when they get back to Naboo and that they enter the gungan sanctuary, I made an audio alteration to your edit to get a Jar Jar voice-over saying “When danger, gungans go to secret place” (I think it works great; I can send a sample to you if you’re interested);
Octorox take on the battle has a very interesting idea to reduce Jar Jar’s antics with the booma without creating a jarring cut;
when Anakin takes the ship to destroy the droids, there is a drop into the sound mix that can be easily fixed (again I can send you the sample I’ve made);
maybe readd the shots of Padmé capturing the vice-Roy since there is a rushed cut to that scene that feels a little bit jarring ?
Reordered some of the final shots of the film so that Padme smiles at Anakin, he smiles back and then Obi-Wan looks away worriedly, foreshadowing the events of Episode II (Octoroxx edit)

And here is a major suggestion I’ve been thinking about: the Gungan underwater scene. I get the theatrical cut is boring and I love how rushed is the beginning of your edit, but I feel for at least 5 reasons it would be good to reinstall a trimmed version of the Boss Nass first meeting (the underwater journey should remain as it is in your edit: totally removed), playing it somewhere in between what Q2 and L8 did:

reason 1: it establishes a first meeting with Boss Nass who plays a major part in the last act (we also get to see the Gungans being technologically advances, hence Padmé’s plan is not that dumb since the Gungans can indeed defend themselves);
reason 2: it gives a quick explanation why the Jedi keep Jar Jar along with them;
reason 3: Obi-Wan’s “What happens to one of you will affect the other. You must understand this.” is an interesting line since it is somehow a meta comment on what’s going on (a very small event will in the end spark an intergalactic civil war over 9 movies);
reason 4: it’s a matter of world building. Gungan City is beautiful and it’s the only city with actual people we get to see on Naboo.
reason 5: Qui-Gonn uses the Jedi mind trick here. It established his grey Jedi behavior as well as something that’s will later be explained as a joke by Watto.

What do you think ? (I know I can be wrong about everything in this post, but I guess now is the time to think everything through one last time for your v4.3 😃).