Also (and I must really stop getting so into this) I watched the 11th Hour again today, and in the hidden room where Prisoner Zero was, when Amy went in there, there was a box, and on the box was a sonic screwdriver. As far as I know River had a sonic didnt she, and she was also in prison, so has she escaped from prison and set about an elaborate scenario whereby she revisits the Dr in another timeline to stop her killing him? Which is not only why she has been hunting him down, but also gave him the coordinates to the graffiti'd cliff face which led him to Stonehenge. Which is where he has hinself been imprisoned.
/head hurty.