I'm still having thoughts about episode 2.
I've just watched it again and, apart from the obvious emphasis on all the mirrors (I'll get back to that in a minute), I made a connection between something eye patch lady said and something the Silent said when Amy was in their spaceship or whatever. It said she'd been there many days and she reckoned she'd only just arrived - the Silent also made her sleep; eye patch lady had said previously "she's just dreaming," so it seems like there should be a link here. Is it possible that some (or all) of the events (such as the orphanage visit) are only just Amy's dreams?
Also, and back to the mirrors (I'm not sure whether this point has been made). In the child's room where Amy got astronaut-ed, we never actually saw he she went from the room to the Silents' spaceship. As we know, she was stood fairly close to a mirror, and emphasising on the points others have made about the mirrors being a door between two worlds, it is possible that Amy travelled through the mirror to the Silents' ship? In that way, you could also say that's how the Silence travel... but that would be a bit too similar to Lily Cole, so I'm probably wrong on that last point. Food for thought though.