I recently replaced the window regulator/motor on both doors. The passenger side closes flush while, but the driver side doesn’t. Would the weather stripping cause it to close short of flush? Or a bad A pillar? The window does roll down and up correctly, just doesn’t close flush and water can drip during rainy days and wind noise can be heard while driving. Any advice or suggestions would be helpful.

 

There are two gold colored screws that protrude on the lower edges of the cover. What you can do is, with the door panel removed, close the door and raise the window all the way up. Have someone take a look from the outside to make sure it's sitting flush as you adjust the screws with a flat head screwdriver.

 

Late but also sounds like u need to do a window motor relearn, so the motor learns the top and bottom limit, plenty of vids on youtube