That isn't good as you know. You say drive flange looks aligned, so it's a bit strange. New engine mounts.... are they handed? on correct sides? Just a thought (I don't have a Marlin BTW). It wouldn't take much movement at the engine mounts to create a large movement on the gear remote, but then (presumably) the drive flange would also change alignment, but maybe to a lesser extent? If nobody comes up with any pointers, is it feasible to loosen mountings and try some movement?
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