There are a few points that can affect the balance in the engine. Couple I saw on here was a high mileage bike that the drive sprocket on the balance chain was indexed due to load because of a bad bearing in the balance cam I think. It had sheared the key drive. Interesting but the user did not realize it. Also, if the alternator rotor has been changed, some are not balanced and that is like another flywheel. One was actually the ECM was bad and one injector was way off.

 

Crank runout, piston weight, stacking tolerances are just a couple of reasons why 1 engine will vibrate more than another.

 

On our 2, we have an 03 and an 00.
Her 03 is a tad smoother. It's stock exc for
(loud a$$) V/H straightshots & K&N.
Mine has 203 cams and T/H exh. Barely
noticeable. Mine is 72-74 mph. Anything above
or below that is fine (until you approach triple
digits) .
I plan on 95" kit & 34T pulley this winter.