Also, considering near the end of The Flesh episodes, the Doctor stated that 'Flesh' Doctor's matrix may survive, was it even the Doctor who got shot in the first place? Nothing that is said in this series seems to be without relevance...
I was enjoying the show until 'Danny Boy' appeared, and then I thought 'Ok, this is getting a bit silly now'. All in all very good, but...
I get the feeling this is all going to be cleared up in 'the forest' for one particular reason. How did River Song know her name if Amy has the Sewn namebadge, and the baby is with the eyepatch woman? Obviously the child must spend some time with the group in order to know what her name is, unless she adopted the name later.
As for the Tardis, I think that will be explained at the end of this series, I personally think the Doctor rigged the Tardis to explode (or the Tardis did it herself) to ensure that the events unfolded as they should.