Finally fixed the problem. Hopefully this will help folks in the future with A-pillar problems.
I had a hell of a time trying to get the driver side A-pillar plastic cover to fit and the longer I looked at it I noticed that the lip and goes under the window channel was getting hung up. This is because the lip that comes off the plastic on that side is TOO LONG!
I took out my trusty file and started taking some of the material down. It took me about 1/2 hour of filing but I finally got it down to the point where the A-pillar was not pushing out from the center and sat flush - FINALLY! As well, that helped me line up the screw holes with the metal window trim on top and the holes I pre-drilled on the A-pillar itself.
Did I say that I hate doing interior work???