[jmatta]

Your first mistake was disconnecting the battery, instead of placing it on a maintainer. You have cleared all the codes in the ECU and have reset to default. There may have been a code in there pointing toward a potential problem that the ECU was compensating for. Now that you've cleared it, the car no longer has the ECU assistance to enable it to run smoothly. My suggestion would be to drive it for a week or so to re-compensate and check for DTC codes...it will take at least that long to bring all values within the ECU to a "ready" status.