I loved the story but I'm not sure about when the Face actually and truly dies in your story. Is it on New New New York as shown on Who? It seems to read that way though the formatting could alter it I suppose. See, I've never bought the Jack = Face of Boe scenario, or at least that The Face truly dies and stays dead on New New New York. We keep being told that Rose used the power of the vortex to make him immortal, a "fixed point" in the universe and that the Doctor and Tardis are strongly affected by that, to the point that they flee from him. If Jack = Face of Boe and the Face truly dies there, then Rose did not make him immortal, he is not a "fixed point", and there is no reason to run from him. If Jack = Face of Boe, is a "fixed point" and immortal, then he would have again returned probably with his whole body regenerated.
I think Jack was just messing with the Doctor with the Face of Boe comment. He was a Time Agent, he would know about the Face, and wanted to wind him up.
Still love the story though, and will be looking forward to the PDF.