Not to say that it's not engines themselves, it could well be - but I've noticed that a huge
amount of the vibration usually associated with the motor is in fact coming from the "rag joint" style kit sprocket adapter (never perfectly aligned) & the dreaded chain tensioner (particularly if the chain is too tight) as the chain rattles over the hard plastic roller.
An example of this would be bike w/a shiftkit (or one w/a sprocket adapter & no tensioner) where the vibration becomes virtually nonexistent in comparison. While it's true a single cylinder engine will always be prone to vibration - I've found it's not usually the culprit for an "unacceptable" amount unless the mounts are so loose that fastener failure is a danger (such as attempts to "pad" the mounts w/soft material like "rubber").
Jus' figured I'd throw that out there as a possible cause