To take apart and put back together, I can do in 4 hours, to just put together, 2hrs tops, this is on a regular truck, but not that different, space is just a little more cramped.
to loose a gear on the injection pump is bull, they probably forgot to put it on-assuming they did it right and removed the timing cover(not the same as the water pump plate).
If the cam wasn't turning, then the timing chain failed. A little unlikely, these are pretty robust chains, and I've installed used rusted chains on junk engines(for play, I can mismatch enough parts from junk engines to get a decent runner for a while)
Another possible scenario is the cam gear wood ruff key sheared, and the the gear is free spinning on the shaft, again not that common....
at $100 an hour, assume shop time of max 5 hours to put together.... $2500 definitely sounds high, but they are probably charging you to pull it all apart again and then reinstall as well....diagnostic time to figure why it won't start.....just another way to get at unsuspecting customers. I always get a quote in writing, and a written note to call me if there will be extra work involved that increases the original quote, that way I never get any surprises...like a whole new front end and new brakes after having replacing them all 2 months earlier.