Leaking Heater Core...

I have a question regarding my heater core leaking. It isn't the actual core itself, it is rain-water that comes in through the cowl vent. Every time I go out to the car, the floor board is filled with water (I just finished patching the floor, most likely caused by this same issue). We ran a hose over the hood area and windshield to determine the leak, and it turned out that the water is running down the drainage area on either side of the cowl, but instead of draining out of the sides of the car as it should, the water comes out of the sides and back of the heater unit.

Any schematics or info concerning the fixing of this problem would be appreciated.

Thanks
-- Drake