I assume that the Doctor we see shot in episode one is made from The New Flesh.
Interesting speculation elsewhere that The Flesh also ties into Amy in some way, and that she is still being held by The Silence.
It took me a moment to recognise Raquel Cassidy from Teachers.
Looking on The Tardis Index File it seems that one of the background pieces of music is from Resident Evil: Afterlife
Original post on Dreamwidth - there are comments there.