I recently purchased a used 2017 300RR. It has 125 hours on the engine. Previous owner said he has not done anything to it besides oil changes and air filter cleaning. After getting it home, I changed the transmission oil. it was pretty black and there was a good amount of metal shavings on it. I put in some Rotella 10W40 synthetic blend until it started dripping out the seep hole as the manual dictates. I took it out on a test ride and noticed some rattling noise from the engine/transmission. I was not able to duplicate it while on a stand and tell exactly where it is coming from. So I decided to replace the top end. The manual suggests to replace the top end every 60 hours! so it was a little over due... I did not see anything out of the ordinary. all the parts were in pretty good shape.
After I got everything back together and took it for another ride, the noise was still there. Looking into it further, it seems to happen when the transmission is in between having a load and not. I took the clutch cover off expecting to find a warn clutch basket and dirty oil with metal shards on the drain plug again, but the oil was just as clean as when I changed it 2 engine hours ago and the drain plug magnet was clean as a whistle. Clutch parts looked brand new. No sign of wearing. Spinning the center hub back and forth while in gear and in neutral I did not notice any clunking or resistance.
I took off the front sprocket and spun the shaft back and forth while in gear. It sounded a bit clunky. Maybe this is the noise I am hearing?
here is a video of riding with the noise. you can really hear it around the 13 min mark.
any help or advice on this would be appreciated.