I just finished my repairs to the TC today. All in all it took about 15 minutes to fix the problem, too bad the previous owner didn't bother to do it. It would have saved me a lot of time and money.
I found the drain for the cowling on the pass. side completely full of pine needles and tiny leaves. Getting the wipers off was the toughest part of that. They are supposed to just pull off but mine were stuck. Once I got the top half of the cowling off I could clean out the trash. After that mess was cleaned up I could see through the bottom cowling into the inlet for the fan. It was the same, completely full of trash. So I had to pull that off also. Once that was out of the way I could clean the screen and let it dry out. In the mean time I noticed all the foam insulation was rotten and not worth a damn for sealing. So I actually had water coming in from the bottom of the cowl besides the top filling up and then over flowing into the ventilation system.
I clean everything up, dried it all out then replaced all the foam. This took a better part of a full day to do. If the drain was kept clear this wouldn't had been such a PITA.
Now for the carpet; it was soaked to the point that there was over an inch of standing water in the front and the back was up into the electronics of the front pass. seat. Now when I first bought the car the carpet was wet on both sides and they told me they had just detailed it and scrubbed the carpet. 2 weeks later it was still wet and then we got more rain. 7 inches in 8 hours one of the days.
Two weeks later and the carpet was still wet even with heaters and fans. I ended up pulling out all the seats and trim molding to help it dry out and it did no good. The parts that were dry when I picked it up my fingers tore through it, so the carpet was wasted.
I pulled the carpet out yesterday after receiving a new one from Ford, not cheap either. Put fans on the fire wall insulation to get it dry while using towels to soak up the moisture from the foam. The trim molding had started to grow mold besides the whole floor pan. All the leather had spots of mold. While the car dried out I spent all of yesterday and then 7 more hours today cleaning all the leather, wire brushing the rust and sealing it, cleaning the rust from the seat tracks and lubricating them. I got everything to work now but the bolster pumps, cleaned all trim molding, disassembled the all the seat belts and cleaned them since they also had mold growing on them and they were pretty dirty to begin with.
After that it was time to put the new carpet in and reassemble the car. All this could have been avoided if the cowl drain was kept clean. That's the last time I buy a car off ebay and take over someone else's problems.