Hey, cool build so far. I have an F250 gasser built out in a similar way but I like the GM's too. If/when you figure out your leak please post here. I just got my cap (same one as you) installed and while I haven't found any leaks yet I'd like to know where to keep my eye on.
The tailgate rear door aera seems to be a problem. I don't know about the F250 but the 2500HD has huge gaps on the sides of the tailgate. I was told by a few people in the industry that water will come in that aera and wick it's way up the carpet on the topper. I installed a tailgate seal kit (For the 2500HD) Now I will have to wait for warmer weather and rain not snow like it has been doing. I am headed south in a week so maybe it will all work out!