shift problem is related with the shifter shaft , shift fork , shift drum and gears dog . Nothing in relation with top end. When i put the tranny together and the two crankcase, i test my tranny. with the clutch cover removed, chutch removed  and drive chain removed, you should be able to move the shifter by hand simply by turning the transmission shaft to help gear dog to engage you can run through all gears . if the shift drum is suck , somewhere is wrong in tranny and you should split crankcase to inspect each tranny component