I would check the motor mounts/tranny mounts, and make sure they are secure. There should be four of them, one on the right hand fender, one on the left hand fender, one at the front of the tranny, and one at the back of the tranny. If the shop removed the tranny (which I assume they did), they almost certainly removed all of these mounts, and it's possible that one or more of them are not tight or are perhaps misaligned.