I'm thrilled you're doing this. I really wouldn't have had a clue. I see you found a whole lot of extra stuff; I think Sean's breakdown was a great help.
2 versions is really the only way to go. Are you going to put some sort of branching method to watch either version? I really think that the 4 Goblins intro and Faerie dance is essential.
As cool as that Darkness/Blix intro is, it just doesn't work as well as the 4 Goblins intro. Also Darkness' siloloquie 'I require the solace of the night, etc' is repeated to Lily at the dinner table. It also sets up the 'entrance to the tree and Giant Horn' very nicely. Are you going to try clean it up a bit, maybe use as many shots from the existing versions as you can? There's quite a bit of Blix you can use, and most of the credit sequence should still fit. Can you do anything with Darkness' voice, to try and match it to Tim Curry's?
The Faerie dance is referred to so often in the movie, that you really need it there, even in it's raw state. ( Adds more menace to Gump's 'Then it's your death song I'll be playing' and explains the toast ' Dancing Fool'. Oona also mentions it in Darkness' lair; 'I could vex you, dance your life away'. There's abot 30 seconds of footage in the featurette showing the crew filming Gump playing his fiddle during the Faerie Dance. You think you could use this? It's just after Ridley mentions the fire at the Bond stage.
I always wondered if all those shots of restoring the Alicorn would work as a full sequence, not intercut with Jack in the pool. Should be quite cool to see.
Anyway, good luck and hope you get the music cues you need.
PS: What do you think of Screwball's line in Darkness' Lair 'It's Faerie magic' when Oona's secret is revealed? Never worked for me, I mean, Screwball should be quite familiar with Faerie Magic, being a Faerie himself.
Edit: There's also that scream of Lili's when she looks down at the pool after Jack dives off the cliff. Doesn't make sense why she's screaming. She's actually supposed to be seeing the Pool freeze over, but we don't see that. Could you manipulate that scene a bit? I think there's a shot later where you see a half frozen over pool. Maybe bring that shot back to just before Lili's scream?