I made small pilot holes with the coupling on, then slid the shaft back and used a larger bit to make the dimples - probably 1/16" deep, it wasn't precise but didn't need to be.

Great. Thanks - perhaps a small center drill through the coupling to spot it.

Russ is probably right about the size of the key and has given me good ideas on how to go about fixing this problem. I did not know you could move the coupling. I was trying to slide the shaft with the boat in the water, using a hammer and vice grips on the shaft, not an easy task.

Years ago we lost one of the square head bolts. No holes in the head of the hardware store replacement so difficult to wire effectively to the existing bolt. Later lost the key. (Anybody know where these items go when they fall out?) The replacement key may not be the right length. It either slid too far in and disappeared or did not seat properly in the keyway groove.

In 2012 I bought a pack of 5 stainless steel hex drilled head bolts 7/16" x 1 1/2", which are too long, 1" would have been better. I wired SS safety wire though I do not have the tools to do this correctly. Still it lasted five years until this spring. Is it possible using SS bolts is a mistake?

1st. The only problem with SS is that it has a potential to gall. But, you should be ok as is. Frankly, I wouldn't bother but... If you are worried about it you can look into an automotive grade bolt.

Second - you are pulling the shaft through both a stuffing box and cutlass bushing. if you are having trouble moving the shaft forward by hand, 1st position the coupling where you want it on the shaft and tighten it, then get a couple of longer bolts to put through the shaft coupling and into the transmission coupling. Tighten them evenly, a couple of turns on each side until you pull the shaft and shaft coupling up snug to the transmission coupling.
Also, I replaced the 4 nuts/bolts that hold the two couplings together. I used SS bolts and SS ny-lock nuts