Going back to the transmission replacement here... If he removed the transmission, he would've had to remove the transfer case. Is it possible he reinstalled the TC in such a way that caused undue pressure on the front differential?
Makes me wonder if taking it back to the transmission shop is the next step here, since it's too coincidental that this noise started right after you received the truck back from the shop who replaced your transmission.
edited to add: If you take it back to the transmission shop, I would play dumb and tell them you're assuming it's something related to the transmission job. I wouldn't volunteer that you've done everything with the half shaft removal, bearings, etc.