Sorry not enough info. Popping/clunking noise (sounds like gears engaging and disengaging) is in I’m assuming all gears although I did not try to go past 2nd because of the noise. No noise while in neutral It is not u-joint, exhaust or rear bearing related I am familiar with all of those noises and those items have been checked (the noise is coming from under the bike-clutch /transmission area), the noise is consistent while trying to accelerate clutch feels firm bike will engage into and out of gear without a problem. I have already done a search and although there is a lot of good information under that description I could not find anything related to this particular problem.
Pull the entire drive train......including U-joint and the problem should be obvious. I vote for the pinion cup splines. when was the last time the Pinion cup was serviced?