I'm having the same issue right now. I have a 2000 4runner and I am trying to replace the hatch with a 1998 hatch. Ran into the problem of the harness connections not being the same. I don't want to have to rip out the harnesses and try to replace them if there is a better solution. Has anyone gotten around the whole harness swap or had anyone verified that swapping the whole harness will work. Thanks!
UPDATE: You have to swap the entire wiring harness for the rear hatch. All the connections for the lock, window, wiper, etc are the same. The difference is the actual ECU for the entire assembly. I didn't get any pictures but it wasn't too hard. The biggest PITA was trying not to completely break things when pulling the old harness.