2. The Doctor has been actually and consciously involved in the Time War against the Daleks since the second serial of the original series. The Doctor knew EXACTLY where he was, what he was up against, and what he was supposed to do. That's why he sabotaged the fluid link to remain on Skaro until his mission was finished.
The "I started a very long time ago" line from TDOTD could be proof of this.
All the incarnations were involved in stopping the war, so why not involved in the rest of the war?