I have an 06 3500 Mega. I had the same problem, only not as severe. It made a lot of wind noise when I had the TC on, especially when going against a strong wind. Not a problem when pulling the fiver or running empty (unless the wind was real strong and from the exact right direction). Apparently this is a common problem with Dodges/Rams.
Checked with a stealership and the fools said to open door, put the window down, put a piece of lumber between the door and the body, then just heave against the top of the door (in other words, bend the top of the door in). Needless to say I did not attempt.
I was getting some other work done on the truck and spoke with my mechanic about the door. He tightened the door. I did not see how it was done, but apparently this is not a simple process (at least not for me). He told me that there are shims used for adjustment and they are glued in. The hinge bolts have to be removed and the shims separated/removed,then the bolts put back in. It is a trial and error process until the door is properly fitted.
I have no idea if the above info is accurate or not. I would suggest talking with a body shop about how to make the door adjustment prior to attempting. Maybe even get an estimate. Hope this helps in some way.
