You can balance the pistons to the same weight but it takes a special fixture to do the rods. Then it takes a balancing machine to do the crank. They also spin the balancer and the flywheel adding or removing weight as necessary. If you have lightweight rods and pistons they can take weight off the crank throws by drilling. If they have to add weight, they use special metal called Mallory metal that is heavier than the iron in the crank. Quite expensive!
Balancing an engine properly is a machine shop job and cannot be done in the home shop.
Here's a pretty good article about engine balancing:
http://www.hotrod.com/how-to/engine/ccrp-0803-engine-balancing/
