Start at the fly wheel, no gasket, no mess. Clean everything up good so you don't get dirt in anywhere. Pull flywheel cover and spark plug. Turn engine by hand both directions, trying to detect origin of sound. Wiggle flywheel up/dn, in/out, checking for any play. If nothing detected proceed.
With petcock off, flip on side (no oil draining), pull clutch cover. Roll engine with clutch (both ways) checking for sound. Check that nuts on all shafts are tight. Closely check gear and bearing for counterbalance shaft. That gear has three rubber cushions in it. If more than a hair movement back and forth, consider replacing.
If still nothing determined, pull both gears from crankshaft and rotate crank by Fwheel. That will determine whether it's engine/crank related or something in the driveline.
Alternative to clutch cover, pull the head and check things out first. With piston in middle of stroke see if you have excess play front/back with piston. Look at top of piston/gasket for signs of piston hitting gasket as mentioned.
Makes me think of a Grizzly I bought a stehascope for find errent noise. Other than few spots that were less noisy, most everywhere else was same. Lots of parts spining around in there.
When I find and fix the noise, whoever was right I'll paypal them some quick cash 
