If either the throwout bearing, or pilot bearing are an issue, rear driveshaft, transfer case, transmission, and bell housing all need to be removed.
Why are you so afraid to take it back to the guy who did the work, and let him see whats going on? If this shop is legit, they will take care of it, if it something they did wrong, or used a defective part. On the other hand if you supplied the parts that are defective, now your responsible to eat the cost of a new bearing, and all the labor.