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Threads like this make me glad I ordered mine with no sunroof! Sorry to hear all your hassles with this OP, that would drive me nuts. Hope you find what the hell is stinking up your truck.
If you don't have any dampness in any of the carpet after a rain and you are not triggering it with use of the HVAC system, that just leaves a few options. I know you said that the first shop checked the cabin vents behind the rear seat, but I would definitely be checking that with my own eyes. Fold down the back seat and see if there is in fact no water coming in any of those vents.
How long after it rains does it take for you to get the smell?
You can see the vents if you remove the carpeted piece on the back wall. I think it is just a couple plastic clips to pull out. To replace them, you'd have to slide the bed back.It only takes a few minutes.
I can take the truck through a touch less automatic car wash and before the cycle is over, it’s already smelling bad inside.
I washed my truck with a small power washer, total time on various parts for about 10-15 minutes it it was happening. Maybe not as strong, but also not as much water..
For the rear cabin vents, I suppose I could check those for myself.
I thought those vents were not visible from the inside? Only view from outside with the bed off?