They may have put some tension on the motor mounts when removing the transmission, causing them to bind up. To resolve that, they can perform the powertrain neutralization procedure in the Workshop Manual. It simply consists of loosening all of the powertrain mount fasteners and then re-torquing them to the proper spec.
Would this procedure help a driveline vibration felt in the wheel and the floor in the 45-60 mph range, that is only present when coasting? It goes away with light throttle input. It wasn't there before the trans was out of the truck, and I am assuming its either a trans issue or a driveshaft, yolk etc issue.