At home flywheel balance....

KitCarlson said
Bearings are designed to be free floating to accommodate shaft misalignment. It will wobble around some, unless you desire that.

The amount of weight varies with the location radius. Appying the weight to one side may result in a wobble. An example is the application of weights on inside and outside of tire wheel locations.

Machined parts have tolerances, a dial indicator can help you measure accuracy.

I am a EE, not a ME, best to check with a ME for your balance concerns.
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OK, the only rotating it will be doing is free fall rotation, in other words it won't even even be seeing 1 RPM, so no wobble.

The balance tire theory, I've seen this mentioned before .
Take time to study the flywheel,, do you see weight removed or added to both sides ( crank and pressure plate sides) of the flywheel, like you would see on a wheel? The only place I ever see it removed from is the crank side, so I don't think it's an issue.