Waiting on the report from the driveline shop, but I was going to say the u-joints out of phase.
What are the angles, tail shaft to driveline, and driveline to pinion? Both these should be in the area of 1/2 to 3 degrees, up to 4 or 5 is OK, but 3 is ideal. No other angle matters. Out of phase u-joints can't cancel out each other and will create vibrations. Same with different angles at each end, just not nearly as bad as out phasing. A carrier bearing on two-piece driveline can also make noise and vibration.
A bad pinion bearing can make a lot of noise.
With low gear ratio, the engine is now working much hard to pull the truck at a lower rpm and higher speeds. Check the tune up and spark plug condition, you might be feeling a rough running engine under a load.
