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I have already checked the 'search' feature and didn't find anything relevant so here goes.   When I accelerate through the gears normally say between 1200 and 2000 rpm's I can feel a 'grinding' noise coming from the drive train.....if I pull the clutch in it stops....at 2500 rpm's you don't feel it.   I've checked the primary chain, I replaced the double-bearing inside the clutch hub, checked the main shaft for play but it had none, evrything seemed to be tight but when I re-assembled everything the  grinding was still there!   When the bike is accelerating during this grinding when  I go over bumps in the road the grinding changes in intensity telling me it's in the drive train.... The tranny shifts okay up and down...If I do need a tranny a 6 speed O/D is going in (as soon as I save some money!)............  Any suggestions?

 Assuming all mounts are good and tight so there is no deflection (movement) between engine and trans to throw primary alignment off. Do you show any unusual wear in the primary? especially the back plate.

Along with what Sleeaping Eagle recomends you look at, look also for a loose compesating sprocket. They can make all sorts of racket.