I've been doing research on this all day today and I've come up empty handed. My issue is that when my sunroof is in the closed position it sits about 1/4 inch below where it is supposed to. In order to cut down on wind noise, every time I drive the car I have to tap the open button for half a second in order to get it into the actual fully closed position.

I HAVE tried reinitializing it, several times, with no luck.

I found this thread where user Pennywise is having the same issue, and resolves it using the TSB BO016-16 (Moonroof Stuck/Improper Operation). I followed the TSB, removed the map light assembly, the two side garnishes, the torx screws and the glass.



At this point I noticed that my sunroof and assembly looks vastly different than the way it is shown in the TSB. For one, my roof had 3 Torx screws on either side instead of 2 shown in the TSB.




The centering marks pictured are also nowhere to be found, I think I found them, but it's nowhere near what's pictured in the TSB.







It also seems my sunroof motor is nowhere to be found. I searched all over inside where the map light assembly goes for the gear assembly and motor but it is not there. This is the crucial step i'm at, I have to get it out in order to adjust the rails.

Here's mine compared to the picture in the TSB...




And from the reverse angle...




I found the tag for the sunroof (It's a Webasto Hollandia 700) so I figured that I might be able to find a service manual for the sunroof itself, but I had no luck.



I then remembered that I had a PDF copy of the 2006 4runner Repair Manual, so I found the section on the Sliding Roof Housing (06600210.pdf) and referenced the location of the motor compared to the location of the wind deflector. I found that same location on my truck and it seems like it should be exactly where the TSB describes it (right above the control switches).



I then found this thread mentioning referencing the Haynes manual, so I went out and bought the hanes manual. Unfortunately there is not a sunroof/moonroof section anywhere in there. I flipped through it page by page.

So... my question to you is: where is the sunroof motor so I can remove it and adjust my sunroof tracks? Did I miss something?

HINT:
If the battrey terminal is disconnected or after the jam protection function has operated, the ECU of the sliding
roof motor may not detect the position of the roof glass. If the AUTO operation function is still disabled even
if the sliding roof motor is reset, the hall IC (built in the sliding roof motor assy) for detecting the roof glass
position may malfunction.************ from the 2003 mamual. (misspelling is from the manual!)

I don't have mine with me right now, but is it to the rear of where you removed the overhead console? Covered by the headliner?

Sunroof Recall - Webasto Hollandia - SunroofCheck.com sunroof recall

Hooray!!! A battery disconnect and re-initialize fixed the issue. When I tried to re-initialize it before I started with the slide-open button, not the tilt-up one. Not sure if that was why it didnt work or if it was the battery disconnect that made it work, but either way, problem solved!!!

These are the steps that worked for me:

Initialize the moon roof.
A. Press the moon roof switch on the “TILT-UP” side and hold the button (the button may have to be held for up to 10 seconds).
- The moon roof will lock in the fully tilted up position.
- Then, the moon roof will move down a few millimeters.
B. Release the switch — initialization is complete.
C. Cycle the moon roof through all the operating modes (including auto-open and auto-close modes) to make sure the moon roof functions properly.

Some backstory:
The issue began after I tried to open the sunroof while I had something on the roof rack. When the rear of the sunroof raised, it was prevented from opening completely. It opened most of the way, i'd guess it had an extra 1/4 inch to go when it was blocked.

I felt around inside the compartment, back, front, and both sides and didn't feel anything that resembled a motor or bolts. I also looked with a flashlight and wasn't able to see anything.

So, the original question still stands because i'm curious. Where is the motor?

assuming the webasto sunroof is similar to the factory one the motor location may be on this thread. New Sunroof Doesn't Fit Right - Toyota 120 Platforms Forum on a side note, did you have the sunroof replaced by the recall?

When I purchased the car, the sunroof was installed. I assumed it was stock, but I could be wrong. Is there any way to check?

I didn't get it replaced under the recall, but I did observe the adhesive separation on the sides of the glass when I had the glass removed so i'm going to look into getting it replaced. The pictures in the thread you linked to look vastly different than my sunroof.

reread the recall link posted above, if your sunroof says webasto hollandia 700 its a dealer installed option & not from the factory. that's why it looks different that the pics in the other threads

The back of my sunroof is leaking you can push down on the sunroof from outside and it moves down and up. Is there an adjustment to keep it tight ? Thanks