I don't remember how I did it. I do remember I flattened off the back face by rubbing the casting over a piece of aluminum oxide paper lying on my surface plate. It then got chucked in the 4-jaw, and I "centered" (if you can call it that) the casting by getting the bosses for the bolts that hold the crankcase together to be as much as possible on the same pitch circle when I rotated the casting, leaving the center of the casting to take care of itself (though I must have checked it, a least a little). Then I must have turned the chucking piece...and from there on it gets foggy.... ;D I have no recollection of how I got the other half of the crankcase to line up. I may have turned the mating flange on the 2nd half of the casting so the two would be aligned, then drilled the bolt holes in one half and spotted the locations of the holes in the 2nd half. Or something....
Personally, I enjoyed the challenge of finding the parts inside the castings. The thing I didn't like was the ever-present fear of screwing it up and having to buy another casting for a not-insignificant amount of money.
Several times I would do a setup, then walk away for a while before I came back and re-checked the setup for errors before cutting anything.