I don't have answers to all of these but I'll take a few guesses.
1. I think Masaki was telling the truth, Yottsun saw something frightening, pursued it, Masaki tried to look for him, and then Masaki saw her trauma demon and ran from it frantically, possibly stumbling and causing her minor injuries.
2. I think we really are going to see some supernatural cause for this rather than some scientific explanation. But I think it's going to be revealed that what's happening isn't a deliberate act of a malicious entity, but just a spontaneous occurrence that they are all subconsciously giving rise to. The forest I think is just some kind of catalyst that brings it out in people.
3. I don't know, did he?
4. I think Jack is at large, mostly an uncomplicated psycho who will just show up at times to attack people and keep the story interesting. Eventually someone is going to kill him and it's going to create more Lord of the Flies drama. Maybe Lovepon kills him.
5. The penguin's name is "Tokimune." It's interesting that its name is similar to his. Maybe a childhood toy that he gave a name to.
6. Masaki is a red herring. She's just a strange girl as we saw in the first episode with superstitious tendencies who is inclined to believe in the supernatural, which is why she decided early on it would be a bad idea to leave. This is no different from her thinking it would be good luck if she could hold her breath before getting her food, etc.
7. This one is tough and I wouldn't be surprised if Okada doesn't even know the explanation yet. I think someone was getting the place ready for them. But they also found dust that indicated it was long abandoned. That combined with the trees making them circle around makes it seem like the village is a place where the world doesn't need to remain consistent with itself. Which would be Okada's dream come true of course.
8. I think this is just sloppy writing.