So, I have this theory about the whole Amanda deal. I think she's a diagnostic device. I think Kamsky programmed her WAY before leaving, and to most of his employes she probably looks just like another string of code. But before leaving he developed Connor, which is the latest one, the only that can “see” Amanda because he can “read” that code correctly. I have no idea if I'm making any sense at all, but this was my theory. I have more on the other things you wrote, but i'm out of space!