I had the same issue.
I realized that the bike was jumping out of time because the woodruff slot in the flywheel was not stripped but gouged slightly and the woodruff pin in the crank is also bent slightly. So basically the flywheel had play and was jumping out of time, this is what caused that fucked up noise.
I timed the ignition and slammed the hell out of the flywheel making damn sure it was on the crank taper. Then tightened the flywheel nut on without stressing the flywheel against the woodruff pin on the crank. so far so good. no more weird noise. But it prolly wont last long.
This happend because I was using a piston stop to get the flywheel off and tighten it back. fucked my shit up.