R:

Do you still have the old M/C? If so, compare the relationship of the mounting bolt bosses to the piston location of both cylinders. It is that relationship that led to there being two different pushrod lengths. If the bolt bosses of the new cylinder are higher (closer to the top of the cylinder) than on the old one, the pushrod will be "short". Similarly, if the piston snap ring is located farther down in the cylinder in the new one, then the piston will be "low", and the pushrod will seem "short".