would not a roof leak of any kind show up on the headliner?
i'd be looking elsewhere
there's a youtube video on this and be sure to read the replies...
UPDATE 8/29/18:After some extensive leak testing, my dealership determined that the seam between the roof and side panels had bad welds. It was so bad they ...
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this was the update he posted:
10,034 views Aug 17, 2017
UPDATE 8/29/18:After some extensive leak testing, my dealership determined that the seam between the roof and side panels had bad welds. It was so bad they asked if my truck was in a roll-over accident (it wasn't). These welds are underneath the two weatherstrip channels on top of the roof. Their bodyshop re-welded the seams and my truck hasn't leaked since - fortunately it was covered by warranty.