The manual indicates timing should be checked after an engine overhaul. How likely is it for timing to be out after a top and bottom end overhaul?

Almost certain to be out when you get it back mate, not really difficult to do just another job to add to the list.

Also as you have never ridden the bike how do you know it was right before, a good engine builder would set it for you but best to check it.With the collection of bikes you have a timming light will come in handy and learning how to use it is not hard.