Thanks for the suggestions. I was thinking that I should replace the filter. Can any one think of any other place water could be getting in to the passenger compartment and rotting? It happens when the car sits over night.

1998 Contour SVT Black w/ Blue interior Torsen LSD updated shiftforks Lightened Flywheel, HD Drivelines Optimized Thottle Body 2003 3.0L engine upgrade (Soon to be)