David - does it happen when :
1: Only when accelerating up to speed
2: at the set speed
3: only when slowing engine down
4: all the time
5: Does it do it both hot and cold?
6:What were the clearances on the piston?
Was it bored, was the bore measured top, center and bottom (both front to back and side to side)to ensure it wasn't tapered or ovaled?
7:Are you sure it's not the PTO, (known for this kind of "rod knock / piston slap" noise)? Does it change if you engage/disengage the PTO?
8:Are the driver slots on the flywheel - driveshaft adapter worn?
9:Are you sure the flywheel nut is properly torqued down? and the key is in good shape
Because the Kohler is a single, engine speed is not steady - in every rotation, the rotating assembly speeds up and slows down, which will make anything loose rattle, including clutch, flywheel, driveshaft the change in your pocket and your teeth ...