My 2000 occasionally does the same thing. Here is what I know: my window can be rolled up a little too high if I do not pay attention, and, the forward portion of the window remains a bit low...I can grab the window and physically align it so it seals. Based upon my research, I believe my window mechanism is either broken or the window has come loose from the mount at the forward point. In any case, you and I will have to remove the door panel to inspect and repair. I have not done this work on my Mustang yet, but have had many door panels off and fixed/aligned other windows (starting back when autos were made of steel and wiring harnesses caught fire)--so this advice...go slow...all the oldish plastic pieces are brittle...and, a little adjustment may go a long way. You may find that a light and inspection mirror will help you examine the guts of the door. Good luck.