I make a fixture with the centering cone offset half of the desired stroke, and bolt it to the crankshaft, also a similar device that bolts onto the flywheel flange. The tricky part is getting the fixtures aligned with the crankshaft throws, so each pair of cylinders keeps its 120 degree separation from the other journals. That's where my setup fixture comes into play. It's a pair of big V blocks, mounted on a heavy steel support, and a couple of magnetic dial indicators. The crank is rotated on the main bearings until a pair of journals is pointing straight up, and the offset fixtures are attached, using a very sensitive spirit level to assure they're both perfectly vertical. Then I machine two journals, and reposition the offset fixtures for the next pair.
I leave the roughed-out journals with the altered stroke several thousandths oversize, so any indexing error can be corrected during finish grinding, using the indexing feature of the crankshaft grinding machine.
Jerry