Richard, Before you begin any tear down, verify your valve lash is ok. Listening to your engine if a valve did hit the piston you should hear a misfire and or a popping in the intake or exhaust. In my experience whenever a valve made the slightest contact with a piston, it bent. The result was a popping noise in the intake (if it was an intake valve) along with a slight miss depending on how bent the valve was. Your engine sounds smooth even though it is noisy. Pull the valve cover, check the valve lash, cam timing, chain tension.
Since I'm not familiar with the engine internals and valve angles I'm only giving an opinion based on experience with other engines. Look for the easy things first. If that fails, check for a valve hitting the piston.
Oh and I agree with Ian, don't run it any more.
