CTD, this can be a relatively common problem ... especially after a car has been painted. there are 2 separate types of adjustments - the front window and the rear window. first question - does the angle of the rear of the front window match the angle of the front edge of the rear window. this will tell you if the rear window stops are set correctly.
if the angles align, you should first look at where your front window is on the rear mounting (inside the door - requires door panel removal). if you discover, like i did that the window is as far out (at the top) that it can be ... you then take the rear armrests and side panel off and start to adjust the position of the rear window. you will discover that the two mounts on the rear window can be repositioned in 2 directions (each). these can be a significant PITA. my recommendation is - before you start moving them ... take a pencil and trace around where the brackets are currently positioned. that way you can return to the starting point if necessary.
