Window Stops
I recently did some work on the driver's window of my 98 Coupe with power windows and I'll bet your is the same.
If you take apart the door, you'll find two "window stops" that determine just how far the window can go up. It's basically just a 12mm bolt than you can adjust with a socket. On mine, these were adjustable and had about an inch of room to adjust how far up the window would go.
You MAY be able to adjust that on your car to resolve this. I'd suggest checking the haynes manual first under anything window or power door related to see if it mentions the window stops.
The key to remember is that it's sort of a big project because to get the adjustments, you'll have to take the skin, plus plastic lining off. It's important to be careful taking the lining off because you'll need to put it back on. Let me know if you decide to do this and I'll write up my experience in detail.
Take it easy.