At home flywheel balance....

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.