Measure the pistons without the wrist pins, then measure the wrist pins. Match up the lightest pins with the heaviest pistons and see if you are closer. Ordinarily i wouldn't recommend swapping parts around in an engine because they wear together, but if you have significant wear patterns in your wrist pins or rod bushings they should be re-done anywho.
Either that or take a dremel and carefully and evenly remove weight from the inside of the wrist pins on the heavy pistons. No rocket surgery required.
How are the weights of your rods (small end weights and large end weights vs. total weight)? that's where it gets a bit trickier. The small end weight is reciprocating, the large end weight effects both the rotating and reciprocating balance.
If I were to get serious about balancing an engine that is where my time and money would go. There and the crank/flywheel/pressure plate.
RTOFLMAO, I just went back and read the previous post, the one just before this one. While I agree completely whith the post, I just found it incredibly humourous that someone who is so concerned with balancing the internals of an engine rides a harley! LOL....