The water leak is most likely holes rusted into the channel where the windshield rubber attaches. A repair method we used frequently when I owned a body shop involved removing the glass, sandblasting the flange to get to bare metal, and filling the rust holes with a product made by 3M called "Aluma-Lead". I don't think it's in production anymore, but a suitable substitute would be Devcon Epoxy Aluminum. The alternative would be cutting the rusted metal out and welding in patches, which is a long, tedious and expensive process unless you're doing all the work yourself.
Jerry
