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Initially your car might run rough when power supply is removed from the ECU, for a few mintues the ECU needs to re-learn how to run the engine at idle and in normal operating conditions. If you have ran the engine for a while this should then no longer be a problem. If it persists then there may have been some damage caused by voltage spikes to the ECU.

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Q: Why is your car riding rough after replacing new battery and new alternator?
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Would a bad alternator make a vehicle run rough?

Alternator versus Engine Performance IssuesIn and of itself, a "bad" alternator will not effect the engine performance.That said, IF the alternator is not properly charging the battery, and the BATTERY capacity gets low enough, then the very low power can result in very low spark production at the spark plugs, which will fail to dependably ignite the fuel, AND THEN result in "rough," or no running.So, a "bad" battery itself does not cause rough running, but can lead to battery depletion which can.


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