we have the same problem with the water and have been battling it since we bought the car new. We took it to Ford to have them fix the leak several times and they told us it was fixed each time we found it wasn't. I have not gotton it fixed yet, but I can tell you that there is a tray with a deflector that covers the top of the cabin air filter, this tray seems to be to route the water that comes down the windshield away from the cabin air filter, and to some type of drain down inside the fender. It may be that the water deflector is out of place and the water is getting in behind it or it may be that the drain down below is plugged and the water is filling the area and backflowing into your heater, out through the blower motor, and on to your floor. There are several clips that hold the louvered cover that is over the cabin air filter , if you remove them and lift the panel out you should be able to see the deflector, and if you pour water down the windshield, while you have it uncovered you may be able to find your problem. Good luck