That's interesting mate, you said your chain is good, so how are the sprockets, were they replaced with the chain? How are the sprocket shaft bearings? Also, have you ever checked your primary chain slack? You are probably wondering what drugs I've been taking, but bear with me.
My Suzuki GS1000 has a gear primary drive, but the "Achilles Heel" is the clutch is mounted directly onto the driven gear, and after awhile the rivets that hold the clutch hub to the gear get loose, and apart from lots of clutch rattle, the transmission gets all jerky.
I replaced the hub with one that's been re-riveted, and the transmission is "snatch free". If the primary chains are really stretched, the transmission can get a fair amount of snatch in it too?
Finally, staying with the bearing theme, how are your swingarm bearings and wheel bearings? Cheers, Terry.