99 4runner Ltd, so this is weird Ive been trying to get the rear window to work aswell as the wiper, I know the 2 go hand in hand but check this out, I have the tailgate cover off and I unplug and remove the key cylinder which is seized, I stick the key in and try to turn it and it gets stuck, I might add that the remote is also on the key ring. So while Im trying to pull the key out I hear a beep beep and the window goes down, I must of been pressing the window button on the remote, it scared the crap out of me, the remote doesnt open the doors but makes the window go down, but now I cant get the window to go up. The switch on the dash doesnt work neither does the wiper or the defrost. Im stumped I dont know where to look next, if the window went down that means the wiper isnt interfearing,right.
Help!!!!!!!!!!!!

 

Not sure about your issue with the remote working and switch not working, but maybe this will help you in figuring it out:

 

Thanks

 

Start with the wires under the rubber boot between the hatch and body. Pretty common for those to start breaking.

 

Yes it appears to be a common problem. I am very anxious to get home and look into it.
Thanks