I have a PDF of the screenplay and not much of substance was removed from the final film. I think most of the extra material from the 5:25 cut was the extended battle (as CineCraft mentions) and extensions within scenes (some of which wound up in the short version). The screenplay has one scene where Averill stops off at the widow Kovach's cabin on his way back to Sweetwater to offer his condolences and she doesn't come out, and Averill notices somebody following him in the distance (this turns out to be Morrison). Incidentally, it's during this cut scene that Averill utters the "widows and orphans" line which is used as voice-over in the final film as he rides away from the woman and her kids along the trail. It's also revealed in the screenplay that Morrison is spying on Averill and Ella when they have their picnic near the river, and during the "break" in the big battle at the end, Averill burries Nate's body (stills of this scene exist). Other than that, there's nothing else I can recall in the script other than an extra line or two of dialogue here and there.
BTW here's some cool photos of the 70mm print of HEAVEN'S GATE stored at the National Archives taken just over a week ago: https://www.facebook...98056944&type=1 The print appears to still have most of its color, and ends with the freeze-frame of Averill still in the cabin of the boat, just like the original VHS release. It also has the subtitles for the immigrant's foreign-language dialogue, but DOES NOT have intertitles (i.e., WYOMING 20 YEARS LATER).
Also re: the outs having been destroyed. While that was reported back when John Kirk did his photochemical restoration in the early-2000s, the Criterion Blu-ray includes outtake footage during the supplements. I wonder where that came from? Maybe the footage wasn't ever junked, just misplaced (like the seps apparently were when Kirk did his work)?