Most likely it’s because the output gear has not been shimmed properly. Different thicknesses of thrust washer are available to reduce set the clearance. Too big a gap and you get the knocking noise which goes because operating the clutch closes the gap. Very common on rebuilt motors and since the shims are only available in a limited range of sizes, not always possible to get rid of it completely. Its an irritating noise but not life threatening.
To fix it you need to remove the clutch which requires a special puller. I am sure you know not to use a 3 legged puller as advised in the Haynes Manual.
Other possible causes are worn main bearings or a worn clutch support bearing in the outer case.
Hope that helps