[thstone]

To explain a little more of what Tommy said...

Yes, it is very common for the engine to run rough after disconnecting the battery because the ECU settings were cleared. As the engine is operated, the ECU adjusts (learns) the engine settings to optimize operation. Those settings are stored in volatile memory so resetting the ECU clears them. Then when the engine starts again the ECU has to use the original pre-programmed settings which aren't optimal for an engine with a lot of miles and many years of wear and tear. The typical result is that the engine runs rough. The ECU will slowly adjust to the optimal settings again as you drive. Give it a few days or so of normal driving and everything should be back to normal.