Leaking when it rains? Where in the hell is this water coming from?

There is seam sealer over the joint where the round sheet metal portion of the cowl vent protrudes up into the cowl area. I had a car where the factory seam sealer dried up and flaked off, leaving seams that weren't water proof. It's worth a look. as well the rust holes shown in the picture above. Sealing the windshield won't fix those.