I'll only say what the issue was with mine, yours could be different since its a 3500. I went through 3 sets of tires before they eliminated the vibration. It seems these trucks are very sensitive to any tire that is close to out of spec. The dealer initially thought it could be something vibrating in my rear under-seat storage bin so that was emptied out and no change. The issue for me was tires and it wasn't easy to find a set that worked. My passenger seat would shake when empty right around 70 mph. I don't think flat spots are your issue, they should be able to sit for an extended period with no issue.
I feel for ya, very frustrating..You should expect a smooth ride, even in a 3500.