Irritating power window problem

I have a 94 GT convert with an odd problem. When you roll the front and rear drivers side window, they don't line up and the front window overlaps the back by atleast 1/2". Has anyone here ever have that problem I'm not sure if its the back or front thats the problem. I have to drop the back window a little to make them line up. Then it starts leaking in at the top. Any help would be great.

How exactly do you do that? Thre are 2 bolts on top of the door that adjust the stops, but I already tried that to no avail. Do I adjust the scissor part, or the bottom of the window where its glued.