A couple minor details
Heh, I know plot doesn't mean a whole lot in stick flicks, but when you name a character try to keep his name throughout the whole movie. His name changed from David (at the beginning) to Daniel (at the end). Another thing is, if religion is so fought against you'd think that the Christian/Catholics wouldn't build a big, fancy church in the middle of the desert where it can easily be seen.
Other then that, there were some pretty nice effects for a stick flick.