I am going to agree with abmar on this one. Any vibration onI beg to disagree. Severe vibration (and I suppose that's a judgement call) isn't normal at any speed with a standard 650 in good condition. Given what you've done to the bike, though, normal rules don't apply.
one of these engines will be a steady progression. Not starting
up and then going away. Barring any weird imput from suspension
at speed or an out of balance condition of tires and wheels.
I would look into these, check timing and balance the carburators if
a twin carburator setup.