You need to take your truck back to the dealer and have them send it to a body shop to fix the problem. This is something that I would leave to the pros AND if your trucks still under warranty you should NOT have to pay for it. I just got my truck back from Ford yesterday. They had to send it to Baxter Auto Body to have them re-align the doors. My driver door would squeak and it was loud in the cab when I went over a bump or a ruff road, sounded like the doors weren't shut all the way. I was constantly checking my suicide doors to make sure they were closed.

Now it is very quiet in the cab and it doesn't sound like I'm slamming my doors when I shut them now. That was something I hadn't noticed before because it had always been that way. The body shop guy told me that the doors were sagging, driver side was worse than passenger and that they tightened them up, but they didn't want to do it too tight because the seals are still breaking in (my truck has about 8k miles), I not sure if its b.s. but the truck is much more quiet now.