Double Cab Leaks?

Does anyone know if Toyota is still covering the seam seal leaks at the rear of the cab. I thought I saw somewhere that they were pulling the bed and resealing this known issue. My dealer of course, knows nothing about it. Any DIY fixes without major surgery?

 

I have a 2006 double-cab Tacoma that has leaked into the rear of the cab for some time now, following heavy rains. After reading some of the suggestions on this forum and several half-hearted tries to fix the leak (with no success) I finally got serious. First, it was obvious that the leak was somewhere near the back of the cab. Based on advice from this forum I suspected the 3rd (center) brake light over the rear window as being the main problem, and maybe the rear window seal as being a problem too. While I was at it I also suspected the 2 clamp-points where my Yakima racks attach to the edge of the roof at the rear of the cab, slightly bending the rubber door seals. It seemed likely that the leak came from some combo of these 4 areas.
So- first chore was to find the leak. I very careful isolated each area and ran a garden hose over ONLY the brake light, only the rear window seal, and only over each of the 2 rack-attach points. Each of these areas was pretty easy to run water across without hitting the other areas, except for the 3rd brake light. I had to make a 'deflector' using duct tape and some plastic flashing to keep water off the window seal here. A picture of this contraption is attached.
All sealed off, I ran the garden hose over the 3rd light, making sure the water hit nothing else. After about a minute, water started to drip down from the upper rear corner of the cab and pool on the floor. So the 3rd light was definitely leaking. I unscrewed the red plastic outer plate on the brake light and the inside was full of water. It was easy to see why - the 2 screws used to attach this flimsy plastic piece are all the way out on each end, and when you screw it shut it tends to bow out in the middle, to the point where water can get in. From there it's easy for water to get into the cab through the back of the brake light. In my case the large rubber O-ring under the red plastic was broken in several places too. I decided not to replace the o-ring but rather caulk the hell out of the whole thing, with several coatings of the best black silicon caulk I could find. It worked - that was several months ago and the problem is still solved.
But there's more : I also tested the rear window seal and both rack attachment points with the garden hose in the same way - and every single one of these areas leaked too! While the 3rd brake light area was by far the biggest leak, the rear window gasket was also letting in a fair amount of water. So I caulked the rear window seal in the same way as the light. All is good now. For the rack attachments there is very little that can be done and these were very minor leaks anyway so I just let those slide.
So these leaks were easily fixed for an $8 tube of caulk.

 

Damn I thought the 3rd brake light leak was only on the turd gens.

 

My selling dealer agreed to pay 1/2 for a replacement rear window, so that’s what I did. About $500.00 for new glass & installation, non slider.

 

I had bought this Tacoma from a friend who had noticed the leak for the past couple of years but had not been able to fix it. Talking to him later he said he'd been trying to tighten the seal on the rear window; but all the while the main problem was really with the 3rd light (but some minor leakage through the window too).
Also, there was a fair amount of rust along the seam weld on the inside of the upper frame of the rear window right behind the 3rd brake light (see attached pic), but as long as the caulk holds I don't think it will get any worse.