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It might well be the tires. I had factory Continentals (255/65 R17) which rode very smoothly, but were soft and had a lot of side sway when towing a heavy load. I replaced them with Michelin LTX M/S (265/70 R17) which are much stiffer. Now I have similar after-vibes and it feels every bump in the road, but it tows a lot better and the Michelins grab the road better. For now, I will keep the Michelins, but the Continentals were very smooth and had no "after shocks"
Sounds like the "vibration" is hitting a harmonic, which is causing the "vibration" to be excessively exaggerated. The root-cause for the vibration could be something very simple (like said above left out dampeners), or something major. Every truck will have it's own unique (personal) frequency - a frequency that the whole truck will "vibrate" at, and changes for each "bump" in the road. this is true for every vehicle, or "thing" in the world. When the vibration reaches a harmonic - a multiple of the frequency, you get excessive and some times out of control vibration, even to the point of self-destruction. Ever see that movie clip of the suspension bridge in Washington state collapse - same thing. Another example of this is the distrotion from your speakers. So, the "fix" could possibly be different for each truck.
Sure hope these problems are all figured out by the time I go to purchase my F150.
I have an O4 SuperCrew XLT 5.4, It drives great. Maybe slightly rough on the transmission from what I am used to with Chevys, but its pretty smooth I guess. It seems like most of the problems involve the fx4 or with suspension upgrades. I bought used, it has 22000 miles on it now. Maybe its a bug that just has to work itself out. If it happened to me, I would just get rid of it, take the loss, it is just not worth the aggravation, especially how **** I am. I would go back to Chevy, were I came from. The reason I got the O4 Crew was its easier with a 7 month old son, and it fits in the garage.