My 1998 4runner ltd has the usual issue with the rear window. I sometimes carry long lumber which I hang out the back window. I found out what happens if you have too much weight resting on the window - one or both sides of the glass will drop down into the hatch. The reason is the window regulator has two scissor arms powered by the motor. At the end of these arms is a spherical pivot bolt which snaps into a plastic slider/roller bushing, which in turn slides/rolls in two metal guide rails attached to the window glass. Too much weight will cause the thin scissor arms to twist and the pivots to pop out of those plastic sliders.

In the future I think I will build a simple wood frame for my lumber to rest on instead of the window glass.

In my case it was simple to remove the regulator cover plates, raise the regulator and glass to about 3/4 closed, and pop the pivots back into their sliders by squeezing with channellock pliers. One of these sliders is cracked but still holding. Others have reported that you cannot buy those sliders or rails for the gen3, only the entire regulator assy. I do see used ones on Ebay. I have to wonder if some other toyota model uses those same plastic parts, otherwise drilling out the pivots and attaching a small ball bearing might be a lasting fix.

Does anyone have a manual page showing all the related parts belonging to the hatch?

 

Toyota 4runner Parts - Toyota Car and Auto Spare Parts Online - Genuine Online Car Parts Catalogue - Amayama

 

Nice diagrams even though many of the hatch parts are now discontinued.