Two possible reasons I can think of, (1) Check the connection under the moulding to the left of the tailgate, it is the same one you would have to dissconnect if you were to remove the "canopy". It might have wiggled loose.
(2) One of the bolts on the driver side that holds down the "canopy" is also holding down a switch that disables the power window and the rear wiper assembly, when removed. If that switch is bad, or you have the wrong size bolt in there, you will get the same problem.
Good luck!!
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85 4-Runner,
New Engine, Auto Tranny ,4" Lift, 32" Tires, Flowmaster Muffler, Suntop Soft Top....BLÅH....BLÅH....BLÅH.....
There Are Few Problems In The Galaxy Which Cannot Be Solved By A Suitable Application Of Concentrated Phaser Fire.