Don't discount the possibility that the Jagman may have stuffed up accidentily. I've seen bearings in backwards, not in at all, cracked during assembly etc over the years. When you're in a workshop with *****in customers, 10 phones ringing and trying to organise stuff it is impossible to keep an eye on everyone.
As disappointing as it all is, I would remove it, (gotta be done anyway), drain all the
oil overnight into a sealable clear plastic container, then arrange a time to be with jagman when he knocks the back cover off for a look. I know I would feel better seeing it with him rather than have an arse/ face saving story that is close but not the whole truth. If he has stuffed up, pat him on the back, 'she'll be right mate, you'll sort it', then wait a few weeks for him to repair/ replace it.
Just for shi*s and giggles tho in the meantime, undo the four flage bolts but leave the flanges touching still, gearbox in neutral, and rotate the shaft as closely as possible to what it would be doing in real life, if it is a bad shaft it should show a clue. As AC460 mentioned, make sure the uni joints are phased correctly.
Once upon a time long ago, an apprentice and I working together on a truck left a diff section plug loose, it fell out 4 km from the shop, the truck drove another 50 km before a slight noise was heard and they pulled up. We refilled it there and drove it back to pull apart in the shop. Only one small bearing was damaged, cost us about $400 including time (1985 ish) to get it sorted. 1900 bills for sub 60 km is absolute frogsh*t. I hope he is a reasonable honest guy and you get it sorted with him stressfree,