stick an outdrive input shaft or alignment tool in it and spin it with starter and see how centered it is...

My coupler the holes are .392. The flywheel has cobores that are .375 a difference of. 017 even if the bolts had shoulder it could only be .375 to fit in the cobores on the flywheel. I made some stepped pins for three holes then installed 3 bolts then pulled the pins and installed the other 3 bolts. I will check the alignment when I install the engine.