I couldn't find much info about where the 5th Gen sunroof drains come out. I knew they came down the A pillars and somehow out the rear (Just like the 4th gens, there's one run through the tool area in the rear). My sunroof was holding water so I knew I had a clogged drain. Turns out it was 1 of 4 that was clogged the others seem to drain out of the pinch welds with no access to the "exit end" - Toyota this seems like a horrible idea.
My Front Driver drain was the one that was giving me issues so I spent a while trying to track it down. I had tried the weedeater string, and even a coated braided steel cable. It seemed to run the same length down each side before bottoming out so I wasn't sure what was causing the clog.
Once I stripped away some of the panels and electronics I pulled the hose out to find the small "filter plug" on the bottom. This is what was causing my tools to bottom out, and it's also what was causing the clog. Mine was packed full of debris. Figured I'd share a photo in case anyone else is having a problem tracking them down.
Thanks for the picture of end of drain tube, I couldn't pull mine out of sealant in frame. I also bottomed out the weed eater line, then resorted to air pressure. My drain hole was under water while I applied about 8psi from compressor. Then I heard a mild slushy pop and water and fine particles blew out on garage floor, standing water gone.
My car sits outside and the pollen gets so heavy the hood turns green, I suspect only 4runners sitting outside for some time have this clogged sunroof drain.
Use caution with air pressure, I started out with about 5-8 psi and it worked. Using a hand pump may even be a better idea so you don't blow the tube off drain pan.
I have a Harley hand pump for air shocks the probably would work.
Another note, don't get fooled by dribbling water coming out, that drain hose holds more water than you may realize and during a heavy rain, it may not handle the load if partially clogged.
The rear driver hose was accessible in the jack compartment, goes into a 90 degree grommet, hardly any dirt and flowed well.
Passenger rear was seen through my 12v power panel (pops out from rt side) goes into same grommet as driver side and it flowed well.
10/2024 My final solution: After all the work above I still had a wet driver side carpet in a recent rainfall which took 4 months to happen again from first attempt to fix.
This time I was determined to remove the plastic filter / plug from end of hose. You can see it in picture above with dark debris at end. It took a little extra force to remove hose from grommet, but I got it out.. Completely clogged up when I removed it, about a quart of water came out. (had tried pouring water in sunroof for test earlier).
I did the same thing on passenger side, and it took less time. Haven't done the rear, mostly because my front drains do most of the work due to slight incline of parking spot.
It's been about a month and three good rains with no problem.
Lesson learned, skip all the tricks with trimmer string and compressed air, just remove the factory plug from end of hose.
If your fortunate to park in a garage, you'll probably never have this problem.