Once you open up the door and see the way the glass attaches to the regulator you will see why the window stops just short of closing. There are two attachment points for the mount that attaches the glass to the regulator. When one breaks it piviots 180 degrees dropping the window about two inchs lower than designed. If I recall the part is plastic....so you will most likely need a new regulator. The Weatherguard might have accelerated the breaking of the regulator.