First of all, welcome.
When I purchased my 4Runner it had manual windows installed by the previous owner, meaning that it had come from the factory with electric windows. It also did not have a functioning rear window, though the motor, regulator, and other internals all looked fine. I am not a fan of crank windows so it was the first thing I changed after buying it. All of the wiring harnesses were still present and when I plugged in the master (driver's side) window switch to test it I was able to operate the rear window. So on my '99 with factory electric windows you need to have the master window switch plugged in to operate the rear window.
If yours also originally came with electric windows I would bet that is the reason your window doesn't go down. I'm curious how it works for 4Runners that came from the factory with manual windows because as far as I'm aware they still have operable rear windows. You can make a thread about the issue so others can chime in too.
Good luck with your troubleshooting.
edit:
There's a really handy search tool you can use to find things like this you're looking for. If you type
Code:
site:toyota-4Runner.org/3rd-gen-t4rs/ [B]rear window not operational[/B]
straight into Google it'll search the 3rd gen forum for that specific string. Much better than the built in search feature.