[strictly]

post a picture of your passenger door (panel gaps) whole door, with panel gap to fender, sill and b post all in one shot.

I would be tempted to take the window frame completly out, check your door opens nicely then (you mention a clunk), make sure its at the right height panel gaps, then refit the window frame adjusting as you go. While you take the frame out, feel for wobble, and see if the bracket which helps hold it position (is not rusted, it is by the speaker in bottom of door).

If its not a frame problem, i have used silicone spray or WD40 with success on the ends of the window glass to make is move up and down smoothly. In your case it sounds like the frame, but you may want to have a quick go.