Have you removed the two seals behind the impeller? If so, and you've removed the oil pump, it seems to me that you should be able to pull the shaft out through the water pump hole.
Here are the directions from the manual
Disassembly / Assembly Process
IMPORTANT: Use the mechanical seal installation
tool to install the water pump seal, PN: 2872010.
1. Remove the coolant from the engine using a siphon, wet/dry vac. or a drain pan.
2. Remove the airbox, exhaust pipe and resonator. Remove
the hose connected to the water pump cover.
3. To access the impeller and mechanical seal, remove the
water pump cover. Discard the water pump cover gasket.
4. Remove the impeller nut, impeller and washers from the
cross shaft.
5. Carefully pry the mechanical seal and seal out of the
crankcase.
6. Water pump assembly is the reverse of disassembly.
Always use new seals and gaskets during assembly.
7. To remove the oil pump, remove the two fasteners then pull the pump / cover out of the crankcase bore. Discard the gasket.
8. To remove the oil pump / cover, remove the two fasteners then pull the pump / cover out of the crankcase bore.Discard the gasket.
9. The cross shaft can be extracted from the water pump side of the crankcase.
10. Assembly is the reverse of disassembly. Always use new o-rings, seals and gaskets during assembly.
11. Install a new seal onto the shaft from the water pump side.
12. To install a new water pump seal, use the seal installation tool, PN 2872010. Verify the seal lips are facing the cross shaft gear.