I think you need to back up, and tear the top end down, as well as remove the side cover and primary components to inspect the crank seal. The fact that you found traces of rubber in the exhaust, and the bike may have partially seized, also indicates a possible pinched head o-ring. Coolant can wash down the cylinder and cause this. Did the rad cap valve blow off from the system being pressurized? Coolant low/dirty?
Could you nave been chasing a power valve rattle from the start? I have never seen a small end/wrist pin get bad enough to knock by itself.
Take some photos. Take your time, and if your not absolutely sure what you are seeing or doing, ask and we will help.
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