I assume the driveshaft shop checked to see that the yokes are properly phased ?...I've seen guys just slap the splined yoke on without looking to make sure the u-joint caps are properly aligned front to rear,not all trucks had them 90 degrees from each other,some had to be offset slightly--others had a keyed spline that only goes together one way--correctly..
I remember a truck with a 2 piece rear shaft coming in my friends shop years ago to get the u-joints and hanger bearing replaced..after it was done,the test ride showed a bad vibration around 50-60 mph..he tore his hair out thinking it had a u-joint with a needle that fell into the cap,etc,ended up taking it all back apart,nothing was wrong with them...
It turned out after consulting a service tech at a GM dealer nearby,the splined section of the rearmost shaft had to be set at 4 splines "off" from 90 degrees ..once he did that,it ran smooth as glass!..the guy also said some trucks needed a 1/2" thick spacer added to the hanger bearing mount,there was a recall (I know this doesn't apply to your truck,just thought I'd throw that in)...
I noticed on my chevy van after I swapped in a different rear axle,and I didn't out the thin plastic or teflon "pads" between the axle housing and the springs,that the axle seemed a lot noisier than it did in the van I removed it from,and had test driven before I bought it to make sure it was good..