I had the same problem last year. Ford told me to have a reading done, the car was fine. I have nothing but trouble with the battery,windows, locks, and radio. I will check into the hole and water leak.
I kind of had the same problem. My locks would go up and down up and down . The problem was water running down the wires when it rained,carwash ,and would go into the sensor box and screw everything up! I had them seal the hole from the wires going through to the door "which was never done at ford!!! has not happened since .Took one day the place I bought the car wanted to take the quarter panel off and keep it for 3 weeks mind you I just bought the thing so dont be afraid to take it some where other than were you bought it.
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Or your window actuator may have a lock up issue/shot. Very common in late model fors cars. Fairly easy fix if you have a set of basic tools a manual for your stang and lastly a replacement part. Try rockauto.com not too expensive there last time I replaced mine in 2006. Was the window having issues prior to it happening or was this issue a sudden thing?
More than likely it is going to be the switch on the drivers side door. The "master switch" if you will for all of the windows. It is possible that the ground connection came loose from the motor, or there is simply a short in the wiring. Nine times out of ten it is just a problem with the switch. Personally I have a 1995 Mustang GT and my rear drivers side window would not go down. I replaced the switch "it will have controls for all four windows" and now it works fine.
If the material is loose from the glass, you have a very common problem. Somtimes it can be repaired with urethane adhesive like is used to install windshields.
If that does not work, you must replace the window unit wich is SEPARATE from the top.
Get instructions here http://www.topgunwon.com/DVD/
you going to have to take it apart to get to it, is not that hard but time consuming; the parts is cheap. The common problems with those is the regulator is worned and need replacing. regulator is a window track, it keep the window in it track and when it become worned it get sloppy. hope that help some