For sure, as soon as you even move the flex around one bolt hole the balance is effectively ruined. The motor will be balanced for the whole rotating assembly (rods, pistons, crank, harmonic balancer and flexplate/flywheel and clutch). They usually mark your flex with a dot corresponding to a mark on the crank. All of this really means shit, as the factory balance was no where near as good as the balance work you have had done. You probably wouldnt feel it, it would probably be better than the old motor you drove. But saying that in a worse case you may feel a vibe if you're really looking for it. If you are really worried take it back in, its only money!!
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