Hold on folks!! Disclaimer: I do this for a living on aircraft, helicopters, propellers, turbochargers, race engines and other spinning things. I recently balanced a Fenestron fan 3200 RPM, 4 foot diameter, with 10 blades, each one in a non symmetrical position! The listeroid balance is child's play.
First off, those flywheels will likey be fine for your application. There is no magic to balancing and some of the methods suggested are not perfect. Using a pen, for example is 100% unnecessary.
Try this, place your trial 2 pound weights opposite the crank throw. There really is no other place that you could possibly need weight. I've never seen an overbalanced Listeroid. Even with huge crank weights. (and I think you don't have a counterweighted crank, hence all the hopping)
Note: if the flywheels are not balanced well, as you suspect, the ideal position for your weight will shift by an inch or two. That's not much and likely within the noise for our purposes.