Sloppy timing chain maybe... I had one that did that, every so many cycles she would pop a little rough and make the chain slap. Is it running even or missing a little? Check the plug and see what its looking like. Might be backfiring a bit also.
I would check and adjust the timing chain and valves. And if you need the manual look below in my sig....
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1984 Honda ATC200ES "Big Red"
1982 ATC200E "Hondie"
1988 TRX300FW "Project Quad" Still in progress....