I've had a problem with water in the spare tire well for some time. A few months back I ordered a used aperture gasket from Miami British. Unfortunately, I wasn't able to make this a priority until this week, with all the rain we've had I vacuumed out about a gallon or so of water from the well.
Before replacing the gasket, I removed several pieces of trim and then placed a hose on top of the truck. With the water running, I could see a steady flow coming in on the inside of the gasket, between the lower tailgate and the D pillar. At first I adjusted the latch so that the lower gate will shut tighter... this did nothing. So, I swapped out the gaskets, applying a layer of silicone on the lip before sliding the gasket over and tamping in place.
I let it dry overnight and just water tested it. There seems to be a smaller trickle, making the turn onto the inside of the gasket just below the latch. I'm going to try adjusting the latch out a bit, to see if the decrease in pressure on the gasket will help. Has anyone noticed this?