I think he is concerned that the thickness of the new flywheel would cause a dynamic imbalance due to the spacing of the weights between the two types. They are a different shape and he does have a point, but the effect is extremely small if you do the calcs (I used assist balancing GM locomotive cranks and blower rotors), I wouldn't worry about it. Balancing is not an exact art and the fact that a crankshaft is flexible except when installed makes it all really a guessing game of pin end weight percentage changes, over balancing and underbalancing blah, blah, etc.etc.etc.
Too much importance is placed on balancing engines especially in magazines, matching piston weights and rods is all you ever need and as long as your crank/rod combo is compensated for (you said he balanced the rotating assy) what more could you ask for, the flywheel is a non-issue if you ask me.
Correct me if I'm wrong on any of these assumptions. <img src="confused.gif" border="0">
“She may not look like much, but she's got it where it counts, kid. I've made a lot of special modifications myself.”
— Han Solo