With your transmission
model number you can look up your bolt pattern. Call a yanmar marine
dealer with it. You need the radius to the bolt centers and the bolt diameters themselves, of course.
Sliding the shaft in/out a bit shouldn't hurt the stuffing box packing too much, if you are just going /out/ with it, just clean up the bit in the boat that will ultimately pass into the stuffing box and now you know you won't be forcing any schmutz into it. Anyways it's an awfully forgiving seal.
It looks like your prop is in an aperture between the keel
? You probably don't have loads of room to work with, then, but you may not need it. You can only go so far until you bump into the rudder
or, in the other direction, bump into the stern (cutless) bearing. The placement of whatever zincs you have will also influence your clearance.
If you have the room, you could simply remove the coupling, bolt the couplings together without it, and off you go. Not if theres not enough clearance between the prop (or any collar zincs) and the stern bearing, however. Clearly you've learned that they are an important engine-saving device, so reinstall a new one ASAP!
These placement constraints also dictate the thickness of the flexible coupling, so make sure the new one isn't so fat it pushes your prop into the rudder, or so much thinner that you hit your stern bearing.
And a change in prop placement can also impact whether your rudder makes contact with it when turned hard over, may want to tweak your rudder stops if so.