Water leak from heater fan into cabin

Every time it rains water pours into the front passenger area through the fan motor for the heater/AC. I removed the cowl and the drains are totally open. My mechanic who has a one-man shop checked the AC drain that enters the engine compartment through the firewall at the bottom of the passenger-side. He used an old dipstick and inserted it into the drain which appeared to be open. I later did the same thing with a wire, but not a wire heavy enough to poke a hole in anything. I then hooked up a rubber hose to that drain and connected it to my shop vacuum and ran the vacuum for about three minutes. No water and no debris came out. I thought a slim chance is that water is getting in at the base of the windshield. I bought silicone caulk and caulked along the base of it. I have looked all around the door and under the hood and cannot find any place that looks suspect.
With the cowl removed there is first the cowl drain tray immediately under the cowl. It has the two drains that I mentioned that are totally clean, as is the cowl tray itself. Beyond that tray, toward the passenger compartment is the air-intake system of openings and sheet metal walls to prevent water from coming into the cabin. When I pour water into that air intake area the water pours into the passenger cabin through the fan the same way it does when it rains. I cannot for the life of me see how water can get back there though during a rainstorm because it looks to me that the cowl tray with the drains open is quite large enough to handle anything but the flood of Noah.