So, here are all the changes that would require manual work, aside from cobbling existing sources together. For ANH, I suppose using NeverarGreat’s Technicolor project (for ANH) would be relatively future proof in executing any of these for the potential use of anyone, if there is desire. (ESB doesn’t seem to require any manual FX work.)

ANH

Ala Adywan, recreate the timing of the crawl in relation to the music (including the timing of Tatooine entering the frame), while retaining “Episode IV: A New Hope.”
This would require tampering with available footage beyond merely selecting between official versions. I would like to use only 2011 footage for the “Look sir, droids” scene, though manipulated to sync seamlessly with OOT timing. The beginning of the shot would need to be extended artificially. At present it would only be possible to do this in a way which is shorter than the OOT. It is minor, but I would prefer not to have this scene come off any choppier than in the OOT, while using only SE footage.
Mos Eisley entrance. This would require some technical work, rather than combining existing official sources. (See OP.)
Use 2011 footage as 3PO and R2 observe stormtroopers interview a man outside the Cantina, though manually remove the trooper dismounting a dewback in an unconvincing manner. Retain the SE dewback, however.
While retaining the SE version of the Alderaan explosion, manually remove the added shockwave.
Depict the Falcon in hyperspace after their escape from the Death Star. (Could be taken from the upcoming Revisited HD Remake, though would be relegated to 720p.)
Ala Adywan, retain the SE Biggs scene, though smooth R2’s vertical trajectory to avoid an awkward jump cut masked by a passerby in the foreground.
Manually fix the SE’s little issue where Leia starts to move her hands upward right as the frame freezes as we wipe to credits.
Manually fix the scale issue between the added Cloud City balcony and our heroes as they run past. (The scene where they meet up with R2.) Could borrow from Adywan, though would need to use the SE’s version of the sky over his for continuity’s sake.

ROTJ:

Either use OOT or apply manual work in order to remove two SE shots of Boba Fett with the SE backup singers.
Use the 2011 galactic celebration montage, modified: Matching the 1997 SE’s timing and audio, replace Tatooine with Naboo manually. (I could probably do this myself.)