'Clunky' Shifts

What are the causes of 'clunky' shifts? I've read that an overfilled primary is the prime cause, but what are other causes? Thanks.

Improperly adjusted and dragging clutch.
Worn out clutch hub bearings ( will cause a growl when taking off from a stop too).
Wrong ( too light ) viscosity gear lube in tranny.
Bent gear shafts (not likely but possible).
Bent shift fork shaft (not likely but possible).
Very worn and tired gear set.

Today, I plan to: drain primary, adjust deflection in chain, adjust clutch at pushrod for 1/2 turn out, refill to bottom of diaphragm spring, and adjust cables for about 1/16" freeplay at ferrule. These changes should improve (reduce) the 'clunk'