I checked out the workprint last night. I did not sit down and watch the entire thing, but just skimmed through to get an idea of what you were doing.

During the TPM prologue, the flashbacks work well but have a few oddities. For one, it really seems to me that Qui-Gon and Shmi are married and that Anakin is their child. This isn't called into question until she asks, "Can you help him?" and he takes Anakin with him. I'm not sure if anything concise can be put in to help this.
The flashbacks don't come off as totally seamless, but I think any viewer would understand what you're doing. I think it works, even if it isn't convincing as having originally been that way. I wish there was a good way to introduce some dialogue into the opening duel. Even just something short with Obi-Wan's name mentioned.

So Obi-Wan doesn't visit Kamino at all. Are the clones ever revealed to be clones of Jango? Is there a line of dialogue that explains this? Again, I didn't actually watch the whole thing. That's my only (small) concern about losing the Kamino stuff.

The romance plot seems to work pretty dang well, and having the primary goal of compressing the story makes this relatively easy.

The aim of this project is to have a three-in-one prequel film suitable for watching in flashback/machete order with the OT, right? Those two viewing orders, in my mind, really highlight the disparity between Padme's death and Leia's vivid memories of her. You know what I did for my edit to address this, but I just want to point it out a something that I notice about the WP.

How's the running time for you? Do you have a timecode in mind that you wanted to shoot for? Of course, the WP is longer than a normal Star Wars film, which might be okay for you.