Did you get them from Twisted Throttle?? If so, give them a call and see if there's any recommendation to be made due to the vibration...
Of course it's a harmonics issue, and I'm sure you're having this issue at certain RPM speeds.. Since there's no chance of being able to travel at different speeds, the trick will be to change the range of vibration on the part, rather than the bike..
caliente cali, kick around the Givi guards.. They say they're made for the Gen 2 bikes, and Sporttour.com has them for $10 less than the SW.. I know nothing about these guards, but Givi stuff is (as well as SWMoto) usually well tested and good quality..
Wonder why they wouldn't fit Gen 1?