I loved the idea of this project but I think the problems you have lie in the restrictions you made for yourselves.

Look at The Godfather Parts I and II.

The structure of Part II only works because of the straight linear narrative of Part I.

So really could leave Adywan's ANH as your part one (with perhaps a few alterations here and there).

Then heavily cut TPM and AOTC to parallel the Sith hunting Anakin and the fear of loss aspects to parallel Luke's story in ESB and the Anakin/Padme love story trimmed heavily to parallel Leia and Han's, Boba's and Jengo's stories would hint at the revelation to come (the son follows the father) and the disarming of Anakin and the unhanding of Luke would serve as the final clue. There's your part two.

The prequel aspects of The Godfather Part II cover Vito from childhood to adulthood and we don't see Luke's childhood so it makes sense to show Anakin's life in the same way.

You already have stated that ROTS and ROTJ fit quite naturally.

So in short I'd leave ANH (though I'd put Boba back into Adywan's ANH to serve as pay off to your next part) and mix selected sections of TPM and AOTC into ESB (minus some of Luke's training) for part 2 and merge ROTS with ROTJ to form your part 3.

That way you don't have to squeeze AOTC in ANH but fit it where it fits best (with a bit of TPM) in with ESB.

I hope you are inspired to return to Reborn as it's an exciting idea and a great way of maintaining the surprises of the original saga while fleshing it out with the best of what the prequels have to offer (while removing the worst excesses).

Best of luck.