I just had a leak in my mega cab. It turned out to be the cab lights. There were hairline cracks in them and they leaked and depending on the incline the truck was parked on, it leaked from the driver's side post that the visor clicks into, or leaked out of the video entertainment system in the back.
Dealer (hopefully) fixed it the other day. Waiting on a good rainstorm to see if replacing all of the cab lights fixed the problem.