I had the same prob with mine about 4 yrs ago all the windows going down and loads of water in the front mainly on the passenger side and to add all the locks locking and unlocking.Searching for the problem i could see that water was coming from underneath the glove box, after about the third time it flooding, the CU board or whatever its called under the unlockable panel on the passengers side helps if you slide the seat forward was bubbling in its own little broth anyway after much worry and torment found out that it was the blocked drain under the drivers wind screen wiper motor arm i found by turning the wipers on and then cutting power when the winderwipers were upright it allowed easier access to the stick that had blocked the drainage hole and loads of leaves. The CU unit has now got a fault were if i leave it plugged in to its multipin socket when i lock the car up the interior light never switches of so i just leave it unplugged and lock all the doors manually and do with out the interiour light i can switch them on manually if needed i have heard of ford dealerships charging silly prices for finding the fault of the dreaded water leak and they know what it is and will charge you for your ignorance the rotten instead of saying there liable to blocking because we only put the tiniest of holes for your water to run down. hope this helps somebody because i can remember how i felt.