I don't own a 4Runner but experienced the same issue (open sunroof... clicking... won't close) with my '04 Highlander. I know it's not a
real SUV but the sunroof components are probably quite similar (as a couple people pointed out with the Camry info.). My first reaction was to search online to learn what others encountered. After picking my jaw up off the floor, I thought I would open up the motor / gear box assembly to see what I was dealing with rather than fork over a pile of cash to anyone. In my case, it turned out to be a fairly simple and straightforward repair.
For the following, refer to
these photos.
I removed two screws inside the overhead sunglasses holder (photo 1) and the trim ring around the interior sunroof opening. Reaching between the headliner and the roof at the front of the sunroof opening (just behind the map light & sunglasses holder), I pulled down a bit to pop the map light assembly loose & disconnected the electrical connector. On my Highlander, there was a metal bracket with a nut on one end to remove. Now the motor assembly held on by two bolts could be removed (photo 2).
There should be two flexible plastic rack gears running through the remaining half of the gear box. I could immediately see that one of the two rack gears was broken and thrashed with the reinforcing wire cables exposed in a knotted mess (photo 3 & 4). The broken rack attached to the passenger side of the sunroof.
With the pinion gear / motor housing removed, the sunroof was easy to move manually. My son pulled the damaged rack end down as I slid the sunroof forward. Admittedly, I was more interested in getting the sunroof closed for minimal expense than trying to achieve a complete repair. I cut off the damaged end (photo 6) so that the broken end could be reinserted through its slot in the gear box (photo 5). I had to move the sunroof back and then forward again to get the broken rack back into position (photo 5).
I could now move the sunroof all the way forward manually but not into the closed (sealed) position. I reassembled everything and engaged the motor to pull the sunroof into its typical closed position. Although the sunroof now works normally (tilts up, slides back and forward), I'm not going to push it. Of course, if I tried to slide it all the way back, it would run past the broken end of the passenger side rack and likely get stuck again. At any rate, I'm happy to have the sunroof closed and sealed without spending a dime. The whole project only took less than a couple hours.
I hope this information is helpful to someone. What I found on the net was helpful to me so I wanted to contribute my experience.