are the roof lines and heights on a 4dr the same as a two door 66? I need to hang a quarter on the car I know I will have to shorten it up by the door but is the angle of the roof pillar the same and in the same location?

Yes if you were comparing a 4-door sedan to a 2-door sedan (post). If you are using a hardtop quarter (that's what is available repro), then I would say that the C-pillar is significantly different the the sedan styles. From what I've seen the angle of the joint between the upper quarter and the C-pillar should be very close if not the same angle, however.
The specs show the same height and headroom front and rear between the 2 & 4-door sedans. To test the theory I have even converted the picture of the 4-door 300 sedan into a 2-door sedan. It looks totally legit.

I have not done this kind of surgery myself, so take it from where it comes from.