My first thought was that there must be a snap ring in there, but I was not correctly envisioning your problem.
The
installation manual shows four bolts joining the above
deck windlass to the frame of the gearbox, with a rather long shaft that must pretty well go through the entire gearbox. It has a very long keyway. That arrangement seems to accommodate different thicknesses of deck.
Given you have removed the
motor, and assumedly the four nuts, but the shaft won't come out, consider this attack: put the nuts back on, loosely, so they protect the ends of the bolts. The pry between the nuts and the gearbox, going around the four in turn.
I'm guessing that the problem is that old grease has become glue.
Flushing the shaft where it goes through the main
gear in the gearbox with penetrant
oil might help loosen the gear from the shaft.
The next round will be for you to come up with some photos - that's the best I can do based on general knowledge of how things go together.