you shouldn't have to in less you accidently shorted something out... Take it some where and see if it has any codes? Autozone and Schucks does it for free or take it to a shop and pay for it, lol.
When you pulled the battery, the PCM lost of its KAM (Keep Alive Memory). Just drive it through a few good drive cycles and the PCM should re-learn the engine.
Check the battery cables for a loose connection and corrosion(incase you didnt clean it). Once running htis normally wouldnt cause rough running, hoever it might expose another issue you have which leads to rough running.
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