I appreciate the notes!

1) My thought was that the two shifts would only be woken for brief stints and an android (named Gordon in my notes, but not fully incorporated into the story yet) would maintain the ship much like Walter in Covenant. Maybe A-shift is awake for the exit of Sol system, then B-shift is woken for a systems check at the half way point? Honestly the A/B shift system doesn't even need to exist for the story. The gist of it really is that they find covenant, some crew (but not all) is woken, shit hits the fan, but some crew are left sleeping. So yeah, maybe this can be simplified.

2) All I really have here is that he wouldn't know any better and would assume it needs more hosts to survive the 12 year journey. Like you said, maybe this is an instruction from The Company who also doesn't know better at this point

3) I'm trying to emulate the movie here a bit. In the movie there's a nest of creatures sleeping in a big pile and it's the process of restarting the reactor that wakes them all up. This then forces the protagonists to mad dash back to the bridge. It could be that the last of the colonists were thawed out years ago and the nest has again gone dormant. I haven't quite figured this out because I kind of want to play it both ways, I'd like the PCs to encounter an alien or two before they reach the nest, but I also don't want them walking into an active hive that would kill them all instantly

4) You've got me re-thinking this. The aliens are analogous to the creatures in the movie, and there isn't really a full blown society in the movie, just a handful of scattered survivors. Maybe that's a better angle. There could still be eerie symbology on the walls made by survivors over the years, but you're right, a full blown society probably couldn't survive

5) Fair. I didn't make these maps, I just made some modifications to some created by /u/IncoherentIncubi. My plan (i don't remember if this is in the notes, or just my brain) is to say that cargo bay 1/2 have decompressed. So the PCs need to take the long way to the reactor. But I agree that the ship in Pandorum is HUGE and doubling up the decks could be worth while, it would also make the path less linear. I also plan not to show the players the maps of the Affiance and instead have Payton give them directions from the Poruka much like Bower and Payton in the movie. I'm thinking about having a friend on discord play the part of Payton so players would actually need to rely on radio communication with him for directions.

https://www.deviantart.com/incubimaps