As of posting I am a quarter of the way through.
You are proberbly going to hate me for saying this seeing as you have done so much work but I think this idea needs a major rethink if it is going to work.
The strength in the crossing back and forth shown in Godfather II was largely down to isolating two characters, father and son.
Here the cutting back and forth becomes very jarring because it's not telling a personal story (or even a couple of personal stories) it's seems that the articles that are being contrasted are periods of time (the fall of the Republic and the fall of the Empire).
And while there are key areas where AOTC mirrors events in ANH there are also equally strong mirror points between events in TPM and ANH. By largely reducing TPM to nothing more than a prelude you are missing out on a lot of potentially useful material.
It might be possible to balance two character comparisons Padme and Leia and Anakin and Luke but to pull that off you would really need to do two different edits blend them together as seperate entities. They would have to be rather radical edits too.
Be more bold with your scene restructuring, be brave enough to not show us that iconic Star Destroyer shot until well into the cut.
Show us Padme growing from damsel in distress to strong leader and senator before contrasting her with her daughter.
Show us Anakin from slave boy to a Jedi in training before contrasting him with his son.
The explanatory text is very intrusive in style and though the content may have worked with the films as they were originally presented it doesn't really serve the viewer in this new context.
May I suggest that you come up with a single crawl that explains that there was a Republic that fell and an Empire that grew in it's place and how the story of two generations play out across these periods.
Once again look at the simple text intro to The Godfather II.
In a few paragraphs we get all we need to know to alert the viewer that he or she is going to be seeing two time periods telling one story seen through the eyes of two characters.
It might be nice to split the screen down the middle and show the slave quarters at Mos Espa with a wind effect and the sound of a baby crying on one side (signifying Anakin's birth) as the text is displayed on a blank card on the other side (just an idea)
As for dealing with TPM look on it in the same way that Coppola does with the young Vito.
Isolate a few moments where we need to see Jake's Anakin and Queen Amidala and build them lead them into their AOTC versions.
We don't need to see the whole of Episode One or Two to get a feeling for these characters, just the key moments that will later chime with what happens with Luke and Leia.
And I hate to say this but some of the music changes really yank these ears around instead of guiding me through the story (the over powering Imperial March when we first see Vader particularly stands out in this regard.)
Remember most people who watch this version will already be familiar with the order of events shown in AOTC and ANH so don't be too afraid to bend the rules a bit and remix the sequence of events a bit more to tell the story in a new way.
I shall report in more as I get through this.