The crank end position had crossed my mind previously, I had an engine builder screw up on thrust washers once, that was a very short lived engine.... You definitely don't want the ZF input shaft inducing any thrust on the crank.
Perhaps you could mate the bellhousing to the engine and mount the starter to see where it engages on the flywheel as a further data point? On that note a spacer between engine and bellhousing would alter the starter to flywheel engagement, but honestly this should be solvable without the need for spacers.