Im thinking its not that they couldnt get it out, they just didnt want to pull the exhaust in order to do it right.
Did this problem develop immediatly after you got it back?
The front shaft is a "slip joint" if that joint is worn it can bang as it turns.
Give it a coat of cheap white paint paint and put it in gear for a couple of turns.
Get under and look for wear marks.
Make sure they actually put the bolts into the crossmember and tightened them.
Make sure thdy didnt whack your trans mount bolts with an impact and pull the threads out of the case or break the mounting block off ( real common )
Hell, for that matter, make sure they put the crossmember back in
I guess its possible that your new found torque skipped the chain.
But I Really, Really ,Really doubt it
Pull the fill plug and stick a screwdriver into the chain and kinda move it around to look for slop.
Dont stick your finger in there unless you dont need it.
Drain it and look for sparkley glitter in the fluid.
But first, go into the lobby of whatever fly by night ********* that had the audacity to rebuild a 4x4 transmission without insisting that they also diagnose the transfer case and driveline before giving you a quote.
And didnt road test the whole system before they sent it back to you.
It could be all random circumstance.
However, I would much more willing to believe that, were it not for the fact that they were either too friggen lazy or stupid to bother googling how to remove the damn drive shaft.
Its not rocket surgery
I hope you got some kind of a warranty.
Dont take any **** off em either.