You could also try grinding the top of the starter plate bell/second speed drive gear/second speed clutch mount plate and second speed gear to lower it so that shoulder is exposed, but then you're decreasing the surface area of the second speed clutch splines.
Or, you could try and make an additional spacer that fits inside the starter clutch bushing to make a new shoulder for the cone to rest on.
My question is, if you stack your cone washer or whatever you're calling it - the spacer that goes between first and second clutch - on top of the second clutch, then first speed clutch, then lock tab and then thread the nut on without the nut going above the bottom of the brash bushing on the bottom of the crank... If you can't then you're going to need even more clearance and certainly not going to be able to come up with just a spacer.
I'd just chalk this up to experience and eat the $150 or however much the crank was and not ruin the rest of your motor and work.