I am going to say you may have an issue with your AWD t case
Engine mounts or transmission mounts
How many miles on this truck?
All 96-01 V8 trucks are either RWD or AWD, full time AWD
When the front d shaft was removed you said the vibration changed, but was still there? It changed how? Remember taking out the front D shaft just removes the power coming from the t case, the front suspension is still a live axle so everything from the tire to the diff on both sides is still spinning.
He has tried different CV axles, he has tried diff set of wheels and tires. I will assume they adjusted tire pressures when doing this to make sure they are all close
New brakes, new control arms, rebiult driveshafts, new suspension parts and alignment, vibration still present.
Some up and down in and out play in the CV axles is pretty normal
Rockauto should take your return? What reason did they give you for not wanting to refund or exchange?
How is the transmission mount? Engine mounts?