I can't see moonroofs changing much. I have expeirence with a 95 Camry and Lexus Moonroofs. My dealer wouldn't help much witout saying that it was going to cost 1200 to fix.
Mine was doing the same thing on my Camry. There are cable dirven regulators on both sides of the moonroof. If one side is trying to move and the other isn't then I would suspect one of the cables in one of the regulators is broken.
The moonroof assembly has to come out. It is time consuming but fairly easy. The bad news is that the whole headliner has to be removed. ON the Camry you take off all the hardware- oh-crap handles, lights, trim etc and the headliner is held on with a hard velcro-type attchment to the roof. Pull firmly and slowly. Try to get one hand in-between the liner and the roof.
I don't have a 4-runner yet.. I am on here cause I am looking at them.
If you have any more questions, send me a private message.
Mike