I bet it stuck and you didnt even know it came off the shaft. The driveshaft is the bottom one, the jackshaft is the top one, the jackshaft spacer does not fit anywhere near as snug as the driveshaft one does, if you didnt pound it off you never removed it so you couldnt have messed up the spacers.
The part to which you refer to the manual has to do with the spacers on the jackshaft,top one that control the spacing for the brake disc as if you dont put them back on the disc will hit/rub on the inside of the chaincase and bind up the jackshaft.