Thanks for a picture of the cotter pin. I had a look at the parts manual but the resolution isn't the best and I'm still not sure of how it locks the shafts together.
It doesn't lock shafts together, it just locks a clutch hub to a shaft. In effect it locks by friction - once the nut is loosened and the pin is able to slide axially as much as the half-moon cutout allows, it is no longer interfering with pulling the clutch off the shaft. The remaining problem is just rust and/or hardened crud that has built up between the shaft and the hub, obstructing sliding. It is desirable to soften the rust or crud rather than use sheer force to pull them apart, because the latter might damage something.
The traditional treatment for your problem is to squirt a penetrating agent onto the junction between shaft and hub, wait the appropriate amount of time (hours, maybe a day) then wiggle the hub both rotationally and axially for as long as it takes. You said earlier that you are getting a couple of millimetres of movement of the hub on the crankshaft, axially. If you have movement, you can get it off without massive force, provided you soften the rust/crud first. The traditional penetrating substance to use is called Penetrene, and you can get it from Repco (and probably other places as well). Cheaper alternatives like WD40 might work also - my own successes have been with Penetrene, and I haven't had any success with WD40, which is mainly intended for a different purpose.
Just get the penetrant into the joint, then wait as long as possible (I've been known to soak a joint for a week, warming it to about 100 Celsius from time to time, but that project ultimately failed anyway - it was thoroughly bonded together). After that is the hard part: the wiggling and twisting, without applying heavy forces because that tends to jam things up. As long as you have movement between the parts, keep wiggling. The wiggle-room will gradually increase.
When the parts are bonded together (no wiggle movement at all) you use a different process, which I won't go into here.
