During the Rainy Season - I found out my '71 Duster had sprung a leak!

I'm the owner of a '71 Plymouth Duster, and so far- lots of engine work, chassis work and I had car painted. I haven't done the interior yet. Very soon the interior will be in the hands of someone who knows what he's doing. I have a VERY good car cover over My Duster, with plastic over the vents on the engine hood, close to the wipers, as I heard that big storms were coming to Los Angeles. Even with all that preparation, our recent heavy rains in So-Cal left the old front carpeting in the Duster-FLOODED. Somehow- Water has come through the vents -under the dash, (the vents with doors that close with levers.)
My Craftsman Wet Vac suctioned one gallon of water from the Driver and Passenger sides of the carpeting.
Question-How is that much water making its way down through those two vents? Car doesn't have A/C. The Heater box was refurbished and installed. New dash vents are attached to new duct hoses to a new heater core.
1.) Has anyone else had this problem? If so-what did you do?
2.) If no one else has ever had this happen to their Duster, any suggestions on how I should proceed?