Make sure the doors are aligned properly and not sagging? Same with window glass, there is minor adjustments that can be made within the door.
I did the drivers door on my old car, never had a problem with the windows but with the windows full up, you really had to slam the door to close it vs. if the window was cracked a bit, air could escape the car and the door closed nicely. I did have to do some tweaking to the window alignment and I also noticed I had a slight sag to the d/s door because after a short while I could see that the w/s was pretty flat again toward the rear bottom of the door.
These doors need a bloody kickstand if you're going to have them open for any amount of time.
I'm new here and not sure if there's a writeup on door and window adjustments somewhere. Been a while since I've done any work of that kind, so I can't recall details for you, sorry.