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After you remove the door panel. and maybe the lower Al cover panel, you will be able to locate the window stops. Most likely you will find the problem and the solution will be evident.
I believe there is a C4 Tech Tip for fixing the loose door panel when it pops off the retainer prongs built into the door frame. Here too pull the door panel to see just what is the condition of the top of that panel.
Once you take the panel off you'll find that there are adjustment screws for several parameters (front travel stop, rear travel stop, angle of tilt) I would recommend that you make only one adjustment at a time and make those adjustments in small increments.
Anyone ever have their driver's side window roll TOO far up? Mine is slightly askew, rolling up more in the front than the back.
Could be the piece of plastic attached to the front of the glass, which is supposed to hit the front stop, is broken. Seems to be fairly common. One of mine was broken off and the other was cracked. I replaced the one and reinforced both with with JB Weld.
Definitely look for broken stuff before you mess with the adjustments. The adjustments are difficult to get right, at least on a vert.