Hi Tom,
First level the rod and put the big end of the rod on a scale to see what that end weighs. Write that number down to remember it. Then make a weight that looks something like a "C" clip that weighs the same as the big end of the rod. Clip the weight to the rod pin on the crank. Level two smooth round bars and set the crankshaft between the rods. Let the crankshaft roll on the main shafts and see where it stops. The heavy side of the crankshaft will be on the bottom. Put a thin felt ink mark on the top of the flywheel and recheck it two or three times to make sure the mark stops in the same place every time. Use a small drill bit and lightly drill the side of the flywheel flange 180* from your mark. Roll the flywheel on the bars again. You may have to do this several times. When the crankshaft is balanced the mark you made will stop in random locations. You should be able to move the crankshaft to any location and not have it try and roll on its own to a different spot. When you have it so it stays in place you can reinstall the rod to the crankshaft. If this is a one cylinder engine the small end of the rod, wrist pin and piston is not balanced because with one piston there is not another piston to balance it to.
Kenny