Holy crap that's a lot. When I got both differentials swapped for Detroit Truetracs (pinion/carrier/ring gear) they were $300 per axle. If they provided the bearings then it wouldn't have been much more but I brought my own.

You can get a mechanics stethoscope at Advance auto parts or Harbor Freight and it beats putting a steel bar to your ear because you can hear everything much better. Get one and touch off on everything that isn't moving from the transmission back when it's on blocks and in gear. I'd put blocks or ramps with a chunk of wood on them under the u-bolts on the rear axle for security instead of just jack stands because they're more stable.

 

My thought was that maybe the bushing in tail shaft and/ or the slip yoke is worn. Did you have the noise before it was rebuilt? Or just after?