You can match up a replacement engine to a Hydra-matic transmission but it takes some special skills and tools.
You can read about it at the link below.
Flywheel housing alignment check
Face runout
Bore runout
http://chevy.oldcarmanualproject.com/shop/1954truck/54ctsm0794.html You also should check the Torus cover runout.
http://chevy.oldcarmanualproject.com/shop/1954truck/54ctsm0762.html Nowadays they make offset dowel pins to help align (dial indicate) the flywheel housing to the replacement engine.
As opposed to drilling, dial indicating and installing oversized dowel pins.
On the engine with no compression, what is the engine serial number that is located on a flat machined boss to the rear of the distributor?
The engine serial number should be some numbers then F54M or T54M.
