Often times the best course of action or the only course of action can be to just cut the shaft out especially if you are paying the labor. The shaft on this boat was 23 years old and had bad cutlass bearing wear and bad stuffing box wear on the shaft. The coupling was so rusted, and space so limited, that the best course of action was to cut it out and have a new shaft made.
Doing this ensures that you will not harm your gear box and you know you are starting with a new fitted & faced shaft & coupling that has no wear and is straight.
*WARNING * WARNING * WARNING: Never, ever let a boat yard use a "SLIDE HAMMER" to remove your coupling. NEVER! The use of these short cut processes can destroy and brinel / create flat spots the bearings or races in your gear box. I have seen yard guys hit them so hard they've actually spit a gear box case in half. CUT THE SHAFT or cut the coupling off before you use a slide hammer.
The shaft, or coupling, is a lot less costly than a gear box. If your yard insists they "do this all the time" it is probably time for you to find a new boat yard. Sorry to be so blunt but this practice is HORRIFYING.