I'm finishing the rebuild on my hangar 9 cub 40 and i'm setting up the aileron throws and noticed that the manual calls for more down than up aileron throw. Its always been my understanding that cubs need aileron differential and to have more Up than Down throw. is it a typo in the manual or is there a reason they did that?

Usually add more up than down with aileron differential. On that Cub, I'd have about 5/8" down and about 1-1/2" up (somewhere around 2:1)