I have a 2008 G35x that makes an annoying clunk when I roll up the driver's window just before its fully closed with the window noticeably moving maybe 1/4 inch forward and back into position just below full closure. I've tried loosening the four track bolts and re-tightening them when the window was fully closed. The window mounting bolts at the bottom of the glass are tight.
The problem is likely related to me unbolting the bolts holding the module base (part 3 in the attached figure). and removing three of the bolts holding the regulator assembly (part 4) to rotate the module base out of the way to reach the door lock linkage that had detached.
Can anyone offer advise on how to correct this problem?

Driver's door glass assembly

 

Your regulator probably just needs adjustment, lower the window so there's about 1/4" gap between the top of the glass and the door frame. It should be the same gap across the top of the entire glass. Sounds like it's probably just tilted a little. All you do is loosen the bolts on the regulator and shift the glass around until it's an even gap then tighten them up again.