There is also a dowel pin in the crankshaft. The pin is for alignment. After you have the bolts out, you might have to thump the flywheel with hammer to loosen it on the pin and crankshaft. Be careful how you handle it- its heavy and the teeth are sharp- or they should be. You probably will have to wiggle the flywheel to get it off the crankshaft, because the fit is pretty snug.
While you are looking around the crankshaft, check the pilot bushing for wear. The inner bore should be smooth, like the bearing surface on the transmission clutch shaft.
Harvester