I've been experiencing horrendous vibrations on my Ten for the 4,000 miles I've covered (owned bike from new).
I had the Yamaha engine bars fitted on the first service and noticed after running it in very bad vibes, especially between about 4,300 to 4,800 rpm. The bars eventually cracked around the centre mounting plate (no surprise there) and I returned them to the shop and had a full refund. Since taking them off the bike has stopped vibrating and feels like a different bike; I can only assume the engine bars are/were the cause of the vibration.