From my point of view, there are two timelines. There's normal historical time, where 1964 leads to 1965 leads to 1966, which us "lower species" think is the be-all and end-all of time, and there's meta-time, where, say, 2005 leads to five billion leads to 1864 leads to 2006, which is what time travelers like the Doctor, Jack, the Daleks, and the other higher-species with first or second hand knowledge of the Time War know of.
Meta-time, like normal time, appears to be a strict progression of cause to effect when examined in isolation. The Doctor meets Jack, the Doctor gives Jack a german bomb, the Doctor rescues Jack from his spaceship when that bomb is going to explode, the Doctor leaves Jack behind on Satellite Five, Jack meets the Doctor in Cardiff and hurls them both to the end of the universe. It's only when you start to mix meta-time and regular time that things get... complicated. Then you get Jack Harknesses popping in and out of time and space like kettle corn, so there were like three or four of him within a few hundred miles of each other at a certain point during World War II. It makes perfect sense from the meta-time perspective, but from the normal time perspective, its downright insane.
Also, you'll note that the only time the Doctor meets someone who is out of sync, like Sally Sparrow or River Song, it's because they aren't time-travelers. It seems there's sort of fundamental mechanic in Whoniverse time travel that prevents time travelers from meeting each other in the wrong order (barring extraordinary circumstances, like every multi-Doctor story ever), but people who stick to regular time don't get that benefit.
In short, the events prior to the Time War will still happen in regular history, even if they take place after events which time travelers claim were before or during the war, like the Dalek Invasion of Earth in 2164 taking place after all of the present-day, post-Time War Dalek stories of the new series. So, in theory, the Doctor could reenter the Time War simply by going to a point before some battle in it took place, and then biding his time and living his way into it, but I presume if he were to try it, those time dragons from "Father's Day" would come out and eat his face.