Just jumping in here because reading your conversation has fired something in my knackered brain -

why are people assuming that the Doctor's Time Lord-y-ness shouldn't be replicable?

Isn't that the reason for burning the body in TIA? I can't remember the exact words, but doesnt older!Canton tell Amy, Rory and River how dangerous his DNA could be if it got into the wrong hands?

What if that's what created the Flesh in the first place and is what he's gone back to fix somehow?