I had a similar problem with my 99. Maybe related, maybe not.
The right rear window would stop when only halfway down. When it was down, the lock would not work, either manually or electrically.
Took the door panel off and found that the pop-rivets that hold the door-lock actuator in place had come loose. I drilled them out and replaced with some sheet metal screws since I don't have a rivet gun.
Maybe your lock thing came loose and was knocked down to the bottom of the door by the window?