First, as to the windwings, I have been told by Rick that the window part and the square channel part that goes into the door are supposed to be all straight and in line. Apparently, with age and closing the doors, most have bent inwards. Yours however sound like they are going out. I do not have an explanation for that. Once I straightened mine out and adjusted the angle from the adjustment where the bottom of the window attaches, I was able to get it lined up perfectly.
Second, as to the windshield, for the Series V, there is a small plastic wedge that fits on the two bolts at the back bottom edge of the windshield between the windshield and the top of the car/dash. This pushes the windshield forward to line up with the windwings. If you are missing this, that would explain why your angles are off. Also, the windshield rake is adjustable by tightening one of the rear bolts more than the other - ie tighten the front one more, it rotates forward slightly, tighten the rear one more, it rotates back slightly.
Hope this helps.
Jay