In an earlier post you said you had fixed your problem. Is it leaking again?
Yes, got back from a 3700 mile road trip where I drove though the rainstorm from Hell in eastern Kansas and Missouri. That rain event was like 50 mph max speed for 90 minutes with cars stopped on the shoulder and under bridges. Afterwards there was some moisture in the carpet pad on the vertical wall. Was much drier than before but still leaking somewhere. So basically a couple likely intrusion point to check now:
1). Still think the access cover to the fuel pump leaks some, has a flimsy foam seal that in my opinion looks pretty much useless. Had resisted the temptation to glue that down with silicone RTV form-a-gasket. In hindsight should likely have done it, rear seat has to come out to gain access to that cover.
2). Some unknown point higher up on the rear cab wall. In discussions when dropping off the truck, the dealership service people and Honda's regional rep seem hyper-focused on the rear window installation seal for some reason.
Further troubleshooting requires disassembling the bed panels and removing all the shrouds surrounding the rear window. So now into a labor-intensive activity with disassembling the bed and leak testing. Not sure yet what will be done about the carpet. Had throughly soaked the padding with anti-bacterial disinfectant cleaners and dried that out. Now when it gets wet, the odor is that of soap (like a freshly mopped floor), no longer swamp odor. Think I could live with soapy odors as long as the leaks are fixed, and not press them to gut the interior to replace the carpets.
Probably should add that while in the rain storm the bed was covered by a soft tri-fold tonneau cover and completely dry inside. The only moisture to challenge the rear wall either came from above the tonneau-level, or draft/splash from underneath. There would have not been any drainage coming from the lower forward bed drains directly onto the pinch-welded cross seam. The only odd variable is that I purchased a set of used wheel & tires in Denver for my Nissan Leaf. Those were stacked in pairs side-by-side in the forward 1/2 of the bed and X-strapped to the forward sidewall tie-downs with ratchet straps. That put some clamping stress against the forward headboard and rear wall under the rear window. That was all under the tonneau cover and bone dry, certainly hope that strap tension wouldn't distort anything to the point of leaking.