Balancing consists of making sure all the parts match, then calculating a bobweight value which is then bolted to the crank during balancing.
With all the parts matching, you can move all the parts around without changing the balance.
Now, as far as the shaking, you'll have to figure out what was happening. If a bad balance, that'd do it, but it could as easily be a bent crank, twisted rod(s), wrong flywheel, etc. FWIW, they can be pretty lopsided before they shake where you can feel it, something is definitely wrong