If the plugs have just been done start looking there... Could be a bad plug with a cracked insulator? Take a look at the burn color? Point a thermal gun at the header and take temp readings. Look for a dead/cold cylinder? It could be a fuel issue, lines or whatever.. Pull the PCV. Nothing personal.. but you need to take it to a good Yamaha dealer/mechanic. Where do you live? I'm sure someone here can help you find a good mechanic/service tech.
The cross-plane shakes a little in the lower rpm but smooths out at 3500 - 4000 rpm. This engine is smother than most inline's. If the motor is shaking badly there is something wrong and you need to get it looked at.