if the engine is in the right spot to start with you can clock off the transmission flange both on the face and spigot, once you do this you will see how central the shaft is to the tube.
you can move the engine around a bit if needed but thats a lot of mucking around to do so expect to do this in the worst case.
just use a dial indicator and collar the boring shaft so it doesn't move back and forth axially, you can even make a mating flange to suit gearbox to the boring shaft and bolt it up but expect some droop due to weight of the shaft which will be reasonably long.
It maybe a method if your chasing a situation where the engine is out of alignment by a lot and trying to get the shaft central to the stern tube, well reasonably close. Just so you know the transmission flange will be in alignment to the bore you make.
