To tell the truth, you have already checked most everything I could think of that is reasonably easy to check.
There is one other thing you could try, depending on your equipment setup.
Its tricky, and borderline dangerous, but is usually gets results.
If you do not have the equipment to do it safely, I'd take it somewhere.
If you can get all four wheels off the ground securely, you can put it in gear and run it up to where the vibration starts and see if you can see or hear what is causing it.
Have someone stay in the truck to stop it if it gets away, and be damned careful about looking under and around so as to not get an article of clothing caught by a spinning tire or shaft.
I had to do that on a lift to find a vibration one time. Turned out to be a rear bent rim.
Another way, which sounds safer, but can be worse if you are not careful is to drive it on a deserted road and have someone drive along side from one side to the other looking for problems.
I have also had someone ride in the back at the same time.
Just make sure that the guy doing the looking is not the guy doing the driving in the other truck.
J.
