to add to the things Darin mentioned, one of the bolts that holds the hard top on also contacts a switch(so no window with top off) if this bolt is incorrect no worky. there should be a window lock switch(is there a hole?)also the relay for the rear window is behind the panel just behind the drivers seat infront of the cup holder thingy.
the backdoor light does not prohibit the window from going up, mine automatically locks the tailgate when the window goes up......Karl