You should have the dealer check the sunroof drainage system just in case. Possible it was hooked up wrong inside of your headliner incorrectly at the plant. Not sure about the t4r, but I have had three other vehicles with sunroof leaks. Usually, there are four drains that ultimately end up either in your wheel wells or in your door jambs. Those tubes are usually slipped onto a nipple the is the original point where the water enters from the sunroof channels. Usually over time, some vehicles systems can come loose at those nipples over time, but I could see how it could be overlooked during manufacturing process. You may be able to check it yourselft by carefully pouring some water into the channels when the roof is open. Then, check to see that the water is draining all out of the wheel wells or door jambs (or wherever they exit the vehicle).
Other thing you might check is your roof rack mounts. After I first put my Baja Rack on, I had a leak in the rear left in the headliner under the mount. I had to remove it, re seal it better, and remount it to solve the problem. That problem was my fault for not being careful enough during original installation of the aftermarket rack, but my point is that water can very easily get in at those points if they are not mounted correctly, factory or not. Those rubber channels along the roof on either side carry lots of water off of the roof, and it has to go around the roof rack mounts.
Hope this might give you further options if the other suggestions don't solve it. My wife's car is in the shop right now for a $2500 repair that originated from a sunroof drainage system defect. Over 8 gallons of water in it after a slew of storms. Ruined the transmission control unit. It was covered under our comprehensive insurance policy thankfully.
Has anybody on here actually serviced their sunroof drainage systems on the 5th gen runner? Especially those who park under a tree all of the time? If not, you need to start doing it! I would love to see some pics of that process...could be very helpful to the members on this forum.
