So chapter one they think it's soras skeleton because that's what the 'parents' tell them, chapter 8 it's implied the parents where killed and put in the coffin but that's not really touched upon when he time leaps back to the funeral.
Now we don't even know if sora's really dead Because turns out it was harukara in the wall, who was working with sora at the time.
This leaves 4 main questions, who was in the coffins, where is sora, what Is the significance of the painting and who's trying to take it. And what happened in Sora's cabin
Edit:
Reading chapter one again shinoharas Expression and his final words being sora murderer implies that sora is the murderer which I'm guessing most people already suspect. He also seems to know a lot more than he's letting on especially about sora and the painting.