Pretty cool! I just watched the parts at the beginning and the end since you said there no changes in the middle.
I think the "Night of the Doctor" sequence would work even better if you put it before the opening credits. That would make it feel more like a prologue and help explain why we never see these actors again. Also, with the title being "Rose," it makes more sense to immediately go to her after that.
Also, after Paul McGann says "I'm a Doctor," the scene abruptly cuts back to the outside of the ship, then back in again. I realize this is because it's after the original credits, and you have to keep the dialogue, so I'm not sure if anything can be done. But since I did notice it, I felt obligated to point it out.
The ending stuff looks fine. The nice thing is that it was already written in such a way that it could have been a one-off after all! And your editing of it was smooth and flawless.
Keep up the good work!