Back in August of 2015 I had to go to some technical training for Ford in Miami. They were nice enough to give me a car for the three hour trip (I live in Tampa), so I left my wagon on the lot at the dealership. It rained hard most all that week and when I got back I noticed two inches of water on the passenger front floor board also the sides of the back seat were wet and the drivers front floor was wet. After some investigation I found at the base of the windshield on the cowl that the fresh air intake duct had no gasket at the base, when the water would shead off the roof and windshield it would run right into that duct filling the air box. Now there is a drain and a baffle in the box but the amount of water was too much with out that duct sealed and it filled the box on the other side of the baffle and leaked between the firewall and the air box on the inside and under the insulation and would go unnoticed until it just flooded that one time. I sealed the air duct and took care of that. The door seals leaked on the rear doors and since the parts manufactures forgot these car ever existed no new seals are available. I removed the seals and with a rubber mallet I gently "adjusted" the pinch weld the seals slide on to towards the door creating a tighter seal. Problem solved for now. The leak on the drivers side front was from a grommet that a vacuum line runs through for the parking brake release. Sealing the grommet took care of that leak. All I have left is the water leaks around the tail gate. I hope this is helpful to someone.
I have the same problem with water leaking into the passenger compartment on the front floor of the driver's side. That air duct stuff, is that on the engine bay side of the firewall, or inside the cabin? I have an 85 custom cruiser, but the design is probably similar.
The air intake duct on my car sits on the passenger side of the cowel at the base of the windshield just under the edge of the hood. The water running off the glass runs under the duct ( when the seal is gone) and into the cabin via the air box. It actually comes out at the recerculation door under the dash.
Sometimes, the drain can get plugged (we in Washington have beaucoups tree needles), causing that exact overflow problem. But also, the cowl is supposed to have its own drain, and if it overflows, it does so into the air box instead of out of the cowling. My '83 CP had that happen during a gullywasher (it's how I learned about the tree needles).
