How is your clutch functioning ?
It is a two-stage clutch, does the p.t.o. stop spinning when the pedal is fully depressed ? If yes, at that time there is nothing turning/moving in the transmission area except the clutch itself.
So could the clutch itself be the source of the knocking ? If it occurs at mid to high r.p.m.'s, maybe it is a broken clutch facing that is forced outward thus hitting the transmission case when subjected to the higher revs.
There is an inspection cover under the clutch if you chose to have a look see.