Here are some instructions I saved from a previous post:
Tim,
I had a similar problem with the driver's-side door on my 99 GTS. Here's how I corrected the problem:
1. Open hood
2. Open door and support with a floor jack (a padded 2x4 placed between the jack and the flat part of the door-bottom worked great)
3. Remove crescent-shaped body panel in front of door to expose door hinges (CAREFUL! There may be shims between the panel and the body that may fall out when you loosen the bolts, so be sure to note their locations)
4. Loosen the hinge bolts and move the rear of the door up slightly (a little movement goes a long way), tighten bolts just enough to check fit, and repeat adjustment as necessary.
CAUTION! Make sure that the window closes properly after adjusting the door. I found that raising the rear of the door caused the front of the window to seal incorrectly at the front; as it turned out, the maximum window height was not properly adjusted, and the window would push the door upright (part containing the door handle) slightly backward when fully raised.
5. Put it all back together (I found that, in order to match the curve of the crescent-shaped body panel to the door, I had to flex the panel slightly before tightening the bolts).
I suppose I could have had this all done under warranty, but where's the fun in that? (and it's a long drive) Good Luck!
Jeff