You have a 2 choices:
1. Just setup the damper and flywheel with the proper external imbalance weights and bolt them on. BUT...BUT...BUT... if you have bored the block and swapped pistons, then a factor called 'bobweight' has changed, and theses standard external imbalances won't be right.
2. To do this per normal balancing procedures, pull the engine, and dissassemble the bottom end. The rods and pistons are balanced against each other per certain procedures, and once that is done, then the bobweight factor is known. That factor is then used with the crank, flywheel, and damper assembled to balance the crank.
Sorry to be the bearer of bad news.