Something is leaking

I second checking the OEM roof rack if you have one. Mine leaked but it was by the pillars not overhead.

 

3rd brake light. There’s a tsb on it.

 

they messed up drilling the holes from the factory

 

Update time.

One of the great things about forums is eventually somebody points out the obvious. I went and sat in the truck and had my son go at it with the garden hose to see if we can reproduce the problem. Funny, cuz in my line of work, we're always trying to reproduce and eliminate failures. Anyways...

The sunroof is leaking, passenger side rear corner. Visual inspection says the sunroof is closing properly, but when he shoots that corner with the garden hose a fair amount pours in. Not drips in. There's like a sheet of water that comes in. I got a business card and stuck it in the gap between the metal and the rubber seal and slid it around. It's pretty tight everywhere except that corner where it's a pretty loose fit. I guess plain old rain can get in faster than the drains can remove the water.

So, this had me thinking...I recall the sunroof motor being all but silent - when it's sliding the glass open it's just the sound of glass sliding on the tracks. In the past year or so I've been noticing when I open the glass I can definitely hear motor/gears. I wonder if something is out of alignment that makes the motor work harder. In either case, it looks like I have a project.

Thanks to everybody for the suggestions!

 

There might be a reset feature.

 

Yet another update in the hope that this helps somebody and I've definitively found the source of the leak and made a solution.

TL;DR
All sunroofs will leak to some extent and the system is designed to accommodate this as everybody has pointed out with the built in sunroof drains. But there are two specific spots on the sunroof where if water leaks water does not fall into the drain channel and under the right conditions could damage the drive belt housing and cause water to fall into the belt housing and drain into the motor, as it did for me. I ended up using some silicone adhesive and 3d printed a diverter to stop this from happening. I've tested and it's a positive fix.

Long story
I had verified that my sunroof water drains are clear. I send down a piece wire and could pour enough water into the drain channel and saw it fall from under the truck to be convinced that there was no way that the rate of leakage around the closed sunroof could exceed the ability of the drain to evacuate the water.

I removed the ceiling console and discovered water was dripping from the sunroof motor. It was also about this time I discovered the one-touch controls on my sunroof stopped working. I could hold and press the button and the sunroof would open and close. I drove around like this for a few weeks of rain and ended up putting a folded towel on the console over night to catch the water. Eventually the sunroof couldn't find the closed position and later the motor it gave out all together. Some nights I would have a wet towel in the morning that soaked through 6-8 layers of bath towel.

By this time I was driving around with the ceiling console removed the whole time. After the motor gave out I just removed the motor assembly all together.

As an aside. The sunroof is opened and closed by a toothed belt that's visible in the gear housing. It's an interesting arrangement where the belt appears to pass side-to-side across the truck but there's belt in the front and a belt in the rear. I can't tell if it's the same belt or not. The motor drives a cog such that when it turns it engages both belts. The belt appears to be fully enclosed except in the gear housing.

When it would rain, water would dribble out of the forward belt guide. Sometimes several teaspoons at a time.

I waited until finally I had a dry weekend to figure out where this forward belt guide goes.

I took the time to drop the headliner in the truck. As somebody else had pointed out, it's rather time consuming but as an advanced DIYer it was straight forward with basic hand tools.

What I discovered was the belt runs to the part circled in red in the photo. It is a U shaped channel with some sort of a cover on top. With a USB endoscope from Amazon and a garden hose I discovered that my sunroof leaks in the corners and water drips directly on to the top of that. Water makes it past the top cover (blue arrow), drips into the channel and straight out of the sunroof motor gear housing.

So, now also armed with the new camera, I was able to better assess the leakage situation. My sunroof leaks in all 4 corners. With the garden hose running with a sheet of water running over the sunroof (remember my truck points downhill when parked) there is quite a bit of water that leaks in. From each corner - imagine your kitchen faucet running at the slowest possible rate where it's a constant stream of water and not drops. That was about the rate at each corner.

Another thing I noticed with the headliner removed. There is a lot of free and unsealed room around the sunroof. If you look down under the air deflector, there is a plastic channel to catch water and divert it to those drains that everybody talks about. But there is at least a half inch gap between the top of that channel and the sheet metal. On the sides, it's even worse, probably about 1.5 inches between the aluminum track and the exterior sheet metal. If your parked sideways on a hill, I really cannot see a reason why water would stay in the channel.

I digress, what I want to point out is that the top of the belt housing is no higher that the top of the plastic channel under the air deflector. i.e. If water drips onto the top of the channel, without it going into the channel, if your facing downhill, water can bypass the channel system entirely and fall into your headliner.

What I ended up doing:
I cleaning the outside of the plastic as best as I could and I sealed it with silicon adhesive/sealant combo. I 3d printed a 1/4" tall lip that sits just forward under the sheet metal that forms a diverter so that water that lands on top of the belt guide gets put back into the drainage system.

yes, my sunroof parts look dirty, and I suspect that's due to all the winter dirt coming in with the water. I take meticulous care of the car and frequently clean the sunroof opening to prevent it from squeaking.

Other fixes.
I noticed a new motor from online Toyota dealers is in the range of $500. I saw on eBay that similar looking motors could be had for about $150. I suspected that Toyota shared parts between large number of their vehicles and I noticed comparing part numbers that the sunroof drive assembly is shared with a number of different Toyotas which meant that despite all the sunroof motors having different part numbers they worked with the same assembly. I ended up using a motor from a Camry and it has worked just fine.

Suspected root cause:
I suspect that water dripped onto the belt housing and got between the U shaped channel and the top cover. During freeze/thaw cycles of winter it eventually broke the seal and the situation cascaded.