After a month of dealing with soggy floors I finnaly got my car fixed. I had taken it into the dealership on Thursday and just got it back today and here is what the problem was. Apparently the machines doing the welding were not up to par the day my car was built. The mechanics at the dealership found gaps in the weld seams along the bulkhead underneath the wiper cowl. They filled the seams with seam sealer and let it sit over the weekend. After all was said and done they tested it and no more leaks. Now I have to say that I also found a problem myself when looking for the leaks. Under the wiper cowl there are clips that hold the cowl on. Under the clips there are cheap pieces of foam that are suppose to seal out water. I took all the clips out and siliconed them in. This stopped the water from coming in around the kickpanel area, but I still couldnt get the water from coming in around the center of the car, behind the heater box. Thats when I called ford and took it in to be looked at. I know there have been a couple other people with that problem, but if you do find that your floors are a little wet take it into the dealer and have those areas looked at and sealed. When I was talking with the mechanic he said there was no information out there yet on this problem, so maybe I am just one of the very few unlucky ones. 
