I just changed a door on a truck. I did not make any window adjustments, but when I lubed the regulator, it clearly looked like there was an adjustment(front and back) for window "tilt". It looked like you could adjust either end about 1/2-3/4"(I did not inspect it that close).
I would simply remove the inner door panel, and roll the window down and look at the mechanism. I would bet you will clearly see what I saw and be able to make the adjustments you need to correct your window fit.