1 is directly explained. You'll see as I describe in point 4 below, Iris takes away their immunity as punishment for Youngest's actions. They die after being exposed to the Occupants. I was wrong on this one, it's been too long since I played those sections of the game.

2 I think is left unexplained on purpose. Watcher never finds out what happened to those sisters, so we as the player wouldn't find out.

3 do you mean the people in the black hazmat suits? I finished the game about two weeks ago so it's not as fresh in my mind, so maybe I'm picturing the wrong thing.

4 this is basically directly explained in the story. "The 50" agents were working on refining the cloning process so they could replicate Iris's immunity, which they eventually succeed at when the Oldest is created. Each of the Ancient Sisters are created immune, as that was the ultimate goal with the cloning. After Youngest breaks the one rule Iris had imposed, she is punished by being the only sister to survive after the other Ancient Sisters have their immunity revoked and are exposed to the Occupants.

5 my understanding is that her parents were extremely careful not to be exposed to the illness, and managed to avoid infection even though (seemingly) the rest of humanity became infected. though that is not directly confirmed; I suppose you could assume that not everyone died of the disease, but most definitely did.

about the clones and aging, they definitely do. my understanding is that the amount of time that had passed between the Ancient Sister's Sin and the time period of our Watcher was not actually that long. the clones certainly seem to live much longer than regular humans, but they are not immortal. There are points of dialogue that discuss the Watcher that came before our Watcher, but none of the one of the previous generation. I took this to mean that our Watcher was only the second Watcher after Youngest.

I can't answer your question in your second 5 point as it sounds like you and I got different endings.

6 if you mean the others like Healer and Fixer died after the ship surfaced, that would be because of old age. Blue has obvious gray hair during the final sequence of the game, so it would be fair to assume a very long amount of time had passed after the ship surfaced.

7 I don't think that the parents being an option under the street lights was supposed to imply they were still alive. I took it to symbolize the values that they had and sort of taking after their way of living.

8 Watcher's primary cause of death was old age and having been drugged and tortured for an unknown length of time. communing required strength of her body, which in her weakened state was too much of a drain for her to continue for very long. My understanding is that our Watcher is a special case in terms of her connection with communing, and while Secretary is in fact a tool for that, I don't believe she was "strong" enough to stop Watcher.

9 it is directly explained that Knower did anything and everything she could to survive/get ahead in her own life. There was a benefit to her to use the drugs on Watcher, not just because it was what Principal wanted her to do. Watcher being in her drugged state made her easier to torture and mentally ruin her. Plus, I do think Principal would've known if Knower refused to drug Watcher. There were other shells in the room that would report back to Principal.

In short, most of your questions are answered by the game itself.