Hi I have a 2006 thruxton and are having problems that feel like a slack chain but it's not I have replaced the rear wheel bearings new cush rubbers and chain and sprockets it appears that when I am riding in a low gear I get harshness coming what appears to the chain but in moving up through them it seams to iron its way out but if I drop the speed down in a high gear the noise reappears then if I change down it seems go away slightly I have checked the main shift with a dial gauge and that's ok So I am at a loss of what to check next
Chain stretch possibly. Is the amount of slack in the chain fairly constant throughout a full rotation?
What Eldon said plus are the carbs in balance? If not it could be running rough at low revs and 'bouncing' the chain. Assume you have used good quality chain and sprockets?