Spoilers alert!
1. Chase is possessed by two ghosts: Sam (the actually good one) and the mirror ghost (from TJ route), the mirror one is probably responsible for Chase killing Sydney back in the day.
2. (I think) the reason Flynn is present in the mines is the same as in Flynn's route, he got there because of his histeria hallucinations that led to safe otter from death.
3. 99% Chase, however as I mentioned before I doubt Chase killed otter without exterior influence (the most probably the mirror ghost made him to do it)
4. There is a lot of ghosts in Echo, Flynn is the one that can travel through timeliness, the "socketface", the very same that Jenna, TJ etc. saw through their life
5. (I think) it is the main reason of the mass histeria beginning. Chase didn't want anyone to know what he did so fatal forces had to make histeria again to reveal truth. I do believe it is the reason, because in TJ route there is no histeria, the most likely reason is because TJ made a game that lead to reveal Chase's murder and histeria wasn't necessary. It wasn't otter's bad energy, it was his sin from the past that lead to this tragedy.
6. I don't understand? The whole plot was that the people trapped in "inception" had to reveal the Jack's? James'? rape on kids? whatever xd. This one that possessed Carl though
If someone see that I made a mistake or has other theory feel free to write it down, there is no plain answer for most of the questions :)