The harmonic balancer is keyed so you can't put it on wrong. The crank pully is perfectly balanced so it doesn't matter how you install it on the balancer.
I would double check to see if the harmonic balancer is on the crank shaft all the way, and you have all the bolts on the crank pully on tight. Any of these can cause vibration. I would also add a drop of lock-tite to the crank pully bolts just do they don't back out.
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