Hi, I'm a new member but have been checking this site regularly for vibration issues. I have found something that might help some of you.
About a month after I bought my truck (new) I noticed an increase in the vibration I felt when going over bumps and stuff. Then I noticed the box shaking like crazy when I looked in my mirrors. I recently found that the support bar going from the quarter panel to the box was loose on the drivers side furthest towards the back of the truck. I loosened the bolt and the cheap clip that the bolt threads through fell apart. Did the same on the passenger side, so I replaced it with a new nut and bolt. The shaking box is much better now and I feel less vibration.

i have a 2006 lariat screw 5.5' box.