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I had the same problem. It was my crank coming apart. Motor sounded like something was hammering bike started to miss shut it off. Waited restarted it then it sounded like there was a nut rattling around. Shut off. Trailered it to my Indy. Went to start it and it locked up solid trashing out the motor.
I had a similar sound on my '03 with 50k mi. High Compression pistons and cams and heads so it is run hard. Anyway I pulled the cam cover to replace the oil pump and chain tensioners. Found the end of the crank running 0.065" out TIR. The flywheel assembly is pressed together and had scissored or twisted over time making the ends of the crank run out of true. The cam plate bushing supports the end of the crank and mine was worn about 1/32" larger than the end of the crank. The tensioners were flexing in and out with the tightening and relaxing of the cam chain. Bottom line is the cam chain flex, tensioner movement, and primary chain flexing tight to loose.
You can detect some flywheel runout in the primary chain case while tightening the compensator. Crank it over and watch the chain, does it go from extremly tight to loose? May want to investigate the cam chest.
Easy to pull the cam cover and check runout of thecrank with a magnetic base indicator.
1 more thing, my son rode this bike 200 miles home from the 110th and all the way home he mentioned the oil pressure was fluctuating at stops and he was having trouble finding neutral.
Apparently the cam/pinion side runout was trashing the oil pump and the crank side was tightening and relaxing the primary chain and having an effect on the clutch basket.
That is what my '03 sounded like, dry knocking sound. I would check your crank runout on the pinion or cam side. If the flywheels have scissored the oil pump is being stressed and if you wait too long the oil pump gearotors will breakup.
Easy enough to pull the cam cover and watch the outside cam chain tensioner. If it goes from slack to tight to slack the end of the crank is not true and the flywheels have scissored.
I don't know if this will help you.... but I just cured a awful clatter/rattle that mine was making. It was so bad I was considering trading it in. Found a small post after many searches and tried this >>>> Marvel Mystery Oil in a spray bottle and since I had seafoam heck I used that too. Sprayed it in the intake and rev'd her up till I used up about 4 ounces and smoked out my yard The rattle is gone. Carbon build-up causing detonation I believe. I have since re-routed the crankcase vent to ground. I am so happy this was a easy fix. I hope yours will be too.
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