The secondary O2 sensor will not usually have an impact on performance, so the misfire was caused by something else and by performing a tune-up, it cleared it. That's always great.
Catalyst system efficiency below threshold can be caused by the problems already specified above. I would start by removing the O2 sensor from the cat (be patient and take your time, use the proper sized O2 sensor socket or wrench) and clean it with a light wire brush and some CRC aerosol cleaner (some people say gasoline works). If you are able to completely remove your catalytic converter, you can hold it up against light and see if the honeycomb cells are still in tact; give it a shake and see if there's loose pieces. If there's loose pieces or melted cells, they it's time to replace it.
Before clearing your check engine light, scan your computer to see if there's additional codes stored. If there aren't any, you can choose to clear it now or have the ECM clear it on it's own.
