Howdy! So it was a long time ago, but I remember reading about some kind of liquid you can put on your window seals to expand them a little bit. Does any one recall what you would rub into the seals?
When I had my windshield replaced a couple years ago, the installation guy (a family friend - got a great deal on that one!) said I could spray and wipe a little WD-40 on the various rubber weatherstripping pieces to help them get watertight again. However, he did say that it was only a stop-gap fix - it swells the weatherstrip up for a while, but then it will dry out and shrink again, and the problem(s) come back.
There is an ecentric type bump stop on the window regulaters that could let you roll the window up a tad farther. I'd look at the door hindges first though.
Anyway ... good luck