Kyle,
I had the same problem you did wth the water in the rear footwell. I cleared those drains but that didn't solve the problem completely. Turns out I had a rot spot near the driver's side hood hinge where a hole through the steel developed. I hadn't been very diligent about clearing up the leaves and debris that accumulate there and the excess moisture eventually led to rot. Take a flashlight and poke around with a long screw driver just to make sure that you don't have a more serious problem.

Alex

__________________
1983 300D (parked for four years)
2012 VW Sportwagen TDI Manual
2001 Miata SE
1962 Chevrolet Corvair Rampside