I think that the issue is that the computer that controls the injection has lost its parameters. Warm the engine up and take the car for a drive. After a bit you will likely find that the roughness will go away as the sensors are able to "relearn" the correct settings. In the future it is best not to disconnect a battery in this for a long period. Swap a battery over any it remembers the settings, leave it for too long and everything is reset.