This is one of those topics that should probably be described in a tech article, since it comes up constantly. Everyone faced with installing a 302/5.0 with the later 50 oz-in external imbalance asks the same question, over and over (including me, 8 years ago).
Late 302/5.0 engines (exact date is the subject of endless debates it seems, but somewhere after 1981 or so) require that both the flywheel (or flex plate, in the case of an automatic transmission) and the harmonic balancer have the correct, later external imbalance of 50 oz-in.
Before that, 302's were the same as 351 Windsors, at 28 oz-in imbalance. And the 351 never did change.
As for your specific balance issue, it's possible (likely, even) that if all the rotating parts were balanced together, then the flywheel was part of that process. Since you need the truck (11") flywheel with the 164 tooth ring gear, if you want the best possible balance you'll need to tear down the engine and get it balanced again with the correct flywheel. Or live with it. Likely it won't be terrible, certainly not as bad as running a 28 oz-in flywheel on a 50 oz-in engine, but if it were mine, my OCD would kick in and I wouldn't rest until it was balanced correctly. But that's just me, an off-kilter old guy...