Doctor Who: Still To Be Resolved...(Part 2)

There's still plenty of threads Steven Moffat has left open for resolution in A Good Man Goes To War and the rest of Season Six, and as the premiere of the former nears closer it's time for some deep investigation:
WHO IS AMY POND? Hear me out- since the character's introduction, Amy has had a crack appear in her wall, the Silence send the TARDIS to her wedding day to explode, the task of returning the Doctor from non-existence after the Big Bang 2 and most recently has been captured by an unknown enemy to produce a baby whose father is unknown, with a Flesh duplicate of her handed to the TARDIS crew to unknowingly stall them long enough for the real Amy to give birth. The question is, what's her significance? Steven Moffat has denied rumours she's River, and I doubt the Doctor would fall in love with River if she's Amy's child, so there must be something else to it, and I have a feeling it's about to come to a head...
WHY DOES RORY KEEP DYING? In Amy's Choice, Cold Blood, Day of the Moon, The Curse of the Black Spot and The Doctor's Wife, Rory Williams seems to die, only to be resurrected in some form. Many writers of this series have said though they cannot be sure, they'd wager Moffat has got something planned that necessitates Mr Pond's numerous demises, and if you can guess a reason I'll be impressed!
WHO SHOT THE DOCTOR? The Moff has said that by the end of this week's episode we will have a "strong theory" of who is inside the Astronaut suit that shoots the 1103 year old Doctor in 2011 USA, but we won't know for sure until the second half of the season airs this Autumn. I would guess it's River as she is in prison for killing a 'good man', but then again she seemed pretty surprised at what happened so perhaps not...
HOW CAN THE DOCTOR SURVIVE? Surprisingly this seems to be one of the questions that no-one is asking and yet is vital to the climax of Series Six, but I'm sure Moffat has a clever way out of Episode 1's shocking twist.
Some other questions to think about: Why is the Eye-Patch Lady making Amy give birth? What does 'the only water in the forest is the river' mean? Why is the Doctor so famous to so many enemies now? What happens if the Doctor gets really angry? And if Amy's house is a two storey building, why are there so many obvious shots of stairs leading to a third floor...?