The rubber seal really just helps wind pass over the seam. The actual waterproof seal is a bead of urethane sealant below the rubber and its what actually holds the glass to the car. They cut through it with a knife, remove glass, then put down new seal and sealant then reinstall. On a 97-03 GP a new windshield is around $200 installed at your place, even if its "with HUD". Remember that before you pay $60 to re-seal it... because with new, you fix the leak and get new seal and glass plus have a warranty against leaks.
Look at the tint band at the top of your winsdhield... is it brownish? If more brown than blue, your glass is past it's life expectancy anyway and you might appreciate a new one if you had it. I recommend stopping by a reputable local auto glass installer for advice since they can look at what you have. I am real happy with the Pilkington windshield I recently got. Different brands are available, check with local installer. My installer used an aftermarket seal that acually fits better than a factory one. Some glass guys know their stuff, and some just slap on windshields then take yer $!