On the side that you suspect is misaligned, does the leading edge of the door glass slide right up the a-pillar rubber seal and stay tight top to bottom? On my car, as soon as the glass starts to come up out of the door, it is at or very near the a-pillar rubber seal and it slides right up it. A misaligned a-pillar would change that. Compare the two sides.
Rodd
Powell, Ohio, USA
1966 230SL, Euro, Auto, Leather, both tops
1994 E420