The ultimate plan is four track, but is probably somewhere in never never land. For now, use existing tracks. Likewise, for some of the grade separations. It is amazing how much NIMBYism comes out, and how irrational some of it is.
As to the creeping in the last couple miles, for the San Francisco end it is near hopeless. The only way to improve the speed into and out of the station is use of larger numbered turnouts in the ladder tracks, and that means making them longer. There is also the small radius curves just outside the station. Maybe the San Jose end could be improved, but I do not know the geography there to comment on how reasonable and likely that would be.