The same thing happened to mine. The tailgate latches have to click twice when it closes. Somehow the left latch only clicked once and the power was cut off to the motor. There's also a switch under one of the bolts that holds the hard top on (third from the back on the driver's side, I think) If that bolt isn't in, the window won't move.

1989 4Runner Special Edition
22RE, 5-spd.
TG 3" SAS, MC DuaLs, 4.56s, Air Locker
Hi-Clearance panels by
www.toyotafiberglass.com