1. Nope, because you can reason it pretty easily in-game. Poor use of context clues is not a failure of writing. She said she stayed because she didn't want to leave him alone.
2. Except Tozu never said they were past events, he said they were secrets. The students also would not assume a pattern because the notes were never shared publicly. For all we know, and they know, half the notes are not about the past. And no, it wouldn't be strange, because it happened. It has already been established Tozu cares more about furthering the game than honesty. It is perfectly reasonable to think one note would be an advantage to kickstart the killing. I have said this multiple times already.
3. No, again. Jury's are not a hivemind. There are PLENTY of occasions of innocent people being given a verdict of guilty. This is just incorrect. No one else would be capable of causing those explosions besides Eva, and no one would be able to see besides Eva, so how she got the tools doesn't matter. Beyond a reasonable doubt.
4. It takes 5 minutes to change a doorknob. Not farfetched at all.