Awesome job so far. That new opening is simply fantastic. The only issues that stand out to me is the pulse rifle effects in 85's death edit. The sound effect for the longer distance shots is a bit too loud and pronounced for the distance the camera is from the rifle, and the sound effect when the camera is close to the rifle sounds more quiet and farther away. Were these effects to be swapped, resulting in 3 lower and one close up at higher volume, I'd say you were dead on. Of course, if the problem is just my speakers, then I do apologize.
I don't mean to nitpick. You're doing awesome work here. And the working list sounds good, all except for removing the junkyard assault, the early encounters with the xenomorph, and Ripley's death.
The junkyard adds more to the movie than it takes. Clemens says, he's going to point her in the right direction, and we get to see where. We also get to see what happened to bishop before he gets plugged in, and it is an emotional scene in the fact that the body of this character we came to respect and know in the last movie has basically been abandoned on a junkpile. It's almost shocking to see. Another thing it shows is that the inmates are truly losing control, and it also demonstrates the authority Dillon has and showcases his abilities as the alpha male and leader. It's not so much that the weak woman is saved by the man, as Ripley gets a good shot in herself, but it does demonstrate why Dillon is not one to screw with, and why he's somewhat in charge.
The biggest reason to keep it though is because without it, Dillon's later comments about Murder, Rape, and brothers in trouble would make no sense at all. I'm referring to the final rumor control scene, where Dillon rushes through his prayer and proceeds to lose his cool before Andrews is killed by the alien. The audience would be left wondering what rape Dillon was talking about.
As for the early encounters with the alien, I think it's the same as Bretts death. The first kills showcase the creatures ability for individuals who may be new to the franchise, and the later scenes where Golic is fascinated by the creature and then escapes and when Murphy falls into the fan would make no sense without them. And honestly, I just think those scenes were very tense and scary and very well done. I do agree about the dog being more shocking though.
And the tunnel chase was just a bad idea to begin with. But they simply had too many characters left and needed a quick way to thin the herd. Had they opted to eliminate the "hell yeah, let's go for it" vibe and instead had them heading through the tunnels because some of the guys on watch had been killed and they were all being stalked, it would've been somewhat better. Or they could've just filmed a scene where Dylan wakes up and one of the inmates is quietly giving him a sitrep, and informs him that several of the guys went missing last night, and that they need to leave the area as quickly as possible. Or maybe Ripley wakes up and Dillon tells her what's going on.
As for Ripley's death, bursting is more gory, but I always found the bursting ending to be a bit too cringy. Her falling and holding that thing was just alittle too much. It happens to burst at that exact moment? And she should have been dead instantly, and not able to hold onto the thing. It's all just alittle too symbolic and cheesy, and kind of screams that you're watching a movie. It's enough for her to know she's going to die, and to fall alive and aware into a lake of molten fire is far more horrifying, sad, and courageous of an end than the counterpart I think. But seeing as how they were bound to (and did) make more movies, I actually would've liked to have her be captured, or at least be injured to the point losing consciousness, and be rescued against her will. Seeing her go through all this hell only to ultimately lose the big objective would've been great.
Maybe that's how they'll do Alien 5. The ending where she killed herself is the dream, and Fury was still real, but the company did get her. Maybe Dillon just knocked her out when she asked him to kill her, everything after that was a dream. Maybe he thought she was now a liability or going crazy and therefore an actual danger to him and his people.
But like I said, fantastic work. I really wish the kind of opening you've created would've been used in the actual film. I look forward to the next edit. It's really cool seeing this stuff.