It has nothing to do with timing. It's a single cylinder engine......vibration is par for the course. Unless it has a counter revolving weight, it will shake. The lighter it is, the worse it will shake.
To dampen the vibes, you must add mass. The pipe frame it sets on, is amplifying the vibrations. The farthest point on the frame away from the origin of the vibration will be the worst, because that is usually where the least mass is.
Ask any Harley rider why they fill their handlebars with silicone or lead shot.
Put a 1" thick plate between the motor and the frame to add mass, it won't go anywhere.