I bet it's the air filter. Take off the cover between the hood and windshield and check out the housing. Water will soak into the insulation under the carpet and run down into the footwell before filling it enough to come up through the carpet.

-Philip Maynard '95 Contour [71 STS | Track Whore] '97 Miata [71 ES | Boulevard Pimp] 2006 autocross results