I got my truck back from the dealership, after they had it for 13 days for a vibration issue.
It turned out the vibration I was experiencing was related to an improper TSB update to my transfer case. Basically, they discovered that the update was applied incorrectly, and that my transfer case has been stuck in four-wheel-high for the past two months. They re-applied the update and now when I run in two-wheel drive there is no vibration. The vibration comes back when I shift to Auto or 4H and cruise at freeway speeds. I was told by the dealership that you shouldn't be driving around in "auto" mode, and just keep in 2H.
Interestingly enough they attributed part of the vibration in Auto and 4H to my "aftermarket shim kit" (aka leveling kit) that has put the front drive axles at a less than optimal angle.
We'll see what the result is going to be in the long term. Hopefully it will be all good.
I have attached the full write up that I received from the dealership, hopefully this will help some of you.