Your exhaust is there for two reasons. The first is noise suppression, open headers may sound cool but is apparently "too loud." The second is to provide back-pressure on the engine. This back-pressure has been calculated and the engine set up to accomidate. Most engines require some amount of back-pressure. By unbolting your exhaust where you did you have changed the back-pressure. In many situations, i.e. adding a better flowing muffler, this can be good and actually produce more horsepower and torque. If you unbolt your exhaust say before the cats, you have almost completely eliminated your back-pressure. This can lead to mis-leading readings on the sensors and cause other engine problems.
As previously stated put it back to how it was. Unless you know how to specifically tune the engine, and can calculate the back-pressure provided, and impliment this into the tuning the best thing to do would be return to stock. If you are looking for a small upgrade buy a cat-back kit. I dont know if a full exhaust system is avialable (manifold back) but i would doubt it.