Ron, I think you can only get close that way. The typical tolerance at the coupling is something like 0.006 inch. And even if you got them back in the exact same spot--and believe me, I tried this myself--you might find that time and deterioration has made the old spots less than perfect anyway.
If you've got a coupling directly to the engine outpu and no plastic drive saver doughnut inbetween, you mainly just need a small enough feeler gauge and some patience as you shove the engine around.
And if we're still talking Yanmar here, you definitely will need to disconnect the shaft, because the post on the mount is pretty high and the engine will need to be lifted up and over it. You don't want to be trying to do that while connected to the shaft.
2000 Beneteau 331
Northern Chesapeake Bay
Ambition is a poor excuse for not having enough sense to be lazy ~ Steven Wright