Just a little note about my roof leak experience. On my '09 1500, I developed the "water leak" almost immediately. Took it back in several times and got the same response everyone got "third brake light". Well, that was NOT the case. After several trips to service, with no solution, I got frustrated and took the matter into my own hands.
The bulk of my water woes came from the driver side grab handle on the A pillar. I literally had water falling out of the bottom screw hole every time it rained. So I took 100% silicone and literally sealed my third brake light. This didn't work.
I went a step further and "sealed" the XM antenna on the rear of the cab, this too did not work.
I had the cab sealing trim replaced with brand new trim. Nope. I went a step further and sealed the trim with silicone on top of the new trim. NOPE.
I thought the windshield might not have been properly set at the factory, so I had it replaced entirely from a windshield company. I watched the guy seal the windshield, he didn't miss a spot. I was convinced this would solve the issue. NOT!
Long story short, the only solution I ever came up with was to take clear silicone and literally run a bead down the entire roof line where the windshield met. After I did this, I never had another issue. Granted, you will need to keep the truck clean or the silicone will eventually look like ****, but at least you don't have water falling.