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Could be historical codes left over from something like running without the mufflers connected. Try clearling the codes and see if they come back. Seems like the codes are saying that you are running too lean. Check for exhaust leaks at all connections and welds. Do you still have the baffles in the SE-2s?
Is the bike running rough? If it is --it sounds like you will have to replace the map sensor. Not a big deal to replace and it might help with the other two codes.