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

To be honest, I have no idea how to get into the Cowl. I can barely even see what is going on from the top vent. Are we supposed to clean it out somehow?
As for the leak, I got under the dash and looked, the water is coming at the bottom corner of the windshield. Or something very near the windshield. So that is not the cowl, correct?
A rust hole in bottom corner of windshield frame area will leak down the side as you described. this is beyond the cowl area and is independent of whether or not your glass is sealed. You would need to remove the trim to confirm.