This sounds like a really cool project, and I'd like to contribute with some suggestions.

1. After mother tells Ripley the auto-destruct-override has expired, there's a shot of her running down a hallway and at the very end of the shot you can see a crew member holding a big black panel. Sigourney hits it and it flops around a bit. You should either get rid of the end of this shot, or edit it to keep the original timing.

2. In the scene where Brett is annoying everyone by constantly saying "right" his cigarette constantly and radically changes length. This could be a tricky fix, and it's understandable if you just leave it be.

3. As Lambert is screaming and Ripley is running to the air canister room, there's a POV shot where you can see the yellow lights on the ceiling going off as if the self-destruct sequence were active. In the very next shot they're not going off. You should probably find a different shot or some behind the scenes footage of the alien to keep the music's original timing. There's some great stuff on the Beast Withing Making of documentary.

4. That shot of Ripley whacking over Ash's head is just awful. It looks ridiculous. There's an alternate take of it that just has Ian Holm's head through the table and Ripley pulling a cord out. It can be found on The Beast Within making of documentary, in chapter 4: "Fear of the Unknown: Shepperton Studios, 1978".