[MENTION=242653]schuler317[/MENTION] Also ... have any other mods/fixes/anything been done that might have affected the wiring / functioning of the affected area? If so... consider revisiting the work to make sure there are no cut or damaged wires or shorts etc.
If that isnt it... do you have access to a code reader? If not, I would suggest seeing if you can get a reliable mechanic / dealer to see if there are any codes triggering ... Long story short, I have had issues with my rear window up/down for years and finally got a tip about checking codes; found an error code triggering and figured out the issue much quicker than I ever could have by tearing apart the back end.
Lastly... somewhere in this:
http://www.toyota-4runner.org/4th-gen-t4rs/100275-service-manual-download-links.html set of posts is a link to get the FSM ... it has troubleshooting sections in it as well ... that might also help you diagnosis and ultimately fix ... You'll just have to hunt through the thread to find the active link as I think the original one is dead.
Best of luck