I had begun to think the car was smelling a bit moldy, but when I felt the carpets, they seemed to be dry. The one day, while driving in a severe rainstorm, I saw water POURING out from under the dash on the passenger side. By the time I got home, I had easily 1-2 inches of water over the carpet on the pass. side.. At first I thought the drivers side was still dry, but when I removed some trim and checked the padding under the carpet, I found that to be wet also. I removed the seats and lifted the carpet up to dry it. I was able to vacuum at least 3-4 gals of water out of the floor pans, and it took another 3 days to completely dry the carpet and padding. (note: The carpet seems to be synthetic, and never felt very wet to the touch. The padding under the carpet is another story)

While the car was drying/airing out, I went searching for the leak. I found a plugged drain hole in front of the windshield under the cowl. Water couldn't drain properly, and then it backed up into the A/C system through the cabin air filter. The drain hole had been fitted with a rubber grommet that seemed designed to trap debris. I removed the grommet and now this drain hole is about 1"x 2" and I feel this problem is unlikely to repeat. I also had to replace the water soaked and moldy cabin air filter. $20.00. But this leak on the passenger side could not explain the water on the drivers side, and I had not seen water coming down from under the dash on the drivers side. The drain hole on the drivers side of the cowl was not plugged when I looked at it.

But now the the drain holes were clear, and I hoped for the best. As luck would have it, one night while the carpet was still up (and the car closed up) It rained. And I had standing water on the bare floor pans the next morning. More troubleshooting with the hose revealed that both side windows/doors were leaking between the plastic weatherstrip retainer and the roof. This seal was designed to leak, relying solely on a strip of foam sealant applied between the retainer and the roof. Mine was either poorly applied at the factory or had shifted over the 4 years the car had been in service. I also found leaks where the door wiring harness enters the cabin through the A pillar (kick panel) That was a real bitch to get to and seal. A fuse box at the kick panel has suffered water damage and shows some corrosion, but so far, everything still seems to work.