Hi, I'm a new member and originally posted this in the 04 and up f150 section, but it should probably be here. I have found something that might help some of you with vibration and or box shaking more than normal.
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 in the rear wheel well going from the quarter panel to the box frame was loose on the drivers side. (the one furthest towards the back of the truck). The bolt was loose enough that I could move the bar freely. I loosened the bolt off a little 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 and removed the broken clip. The shaking box is much better now and I feel less vibration through the truck.

Hope this might help someone.

i have a 2006 lariat screw 5.5' box.