Finally got my car back Friday evening. After those guys taking 4 days just to put in the clutch, they realized friday morning that the pivot ball stud needed to be replaced.
Another problem was they somehow managed to shred the rubber shift fork boot. How does this happen? It's not like it was hard to take off in the first place, so it shouldn't have been under any kind of pull/stress.
The place was called "Certified Transmissions" The appropriate name would have been 'certified idiots'