When you say "just went though the break in period" - how long have you run it? Is it still "4 stroking"? I'd suspect that might be part of the vibe problem, even if it's broken in these things are notorious for runnin' rich and firing every other stroke... Another thing is to double check your rear sprocket mount, if it's offset even a lil it'll shake like a SOB at speed. Spin the rear wheel slowly and watch to see of your chain tightens and loosens - a sure sign of an offset sprocket. Check the motor mounts of course
Vibrations are part of these lil thumpers, realistically - there's not really much to be done other than external "fixes" like soft hand grips and a sprung seat. Your right about "dampening" the vibes though - be wary of the rubber motor mount "fix" in particular as it often leads to other problems like sheared mount bolts and frothed fuel.
Welcome to the forum BTW - good to have ya here!