.002 at the end of the long shaft is not bad at all....002 at the end of the taper on the short shaft would be unusual....Any runout at all would be unusual...If there's a problem it's with the way the flywheel fits on the taper and the surface of the flywheel...The top surface of the flywheel is usually not machined relative to the taper....Even a perfect hub can't track true on a crooked cast surface....
One of the reasons the engines are so cheap in the first place