I recently had a weak battery cause the power steering (EPS) light and the corresponding assist motor to shut off. Talk about an arm workout getting out of the parking lot. Battery recharge and power cycling fixed it.
For your problem I would first see what the CEL is reporting. I don't think a weak battery would cause it to run rough...it sounds more like a bad spark plug or ignition coil, or maybe a dead O2 sensor.
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