41 and 91 are your two O2 sensors. 31 means the EGR valve position sensor, that measures how much the EGR valve is opening, isn't working.
You need to make sure that all the vacuum lines are functional, and attached. If that doesn't clear the code, then unplug the the harness at the sensor, and run a jumper wire between the orange/white wire and the brown/green wire, in the harness connector. Run KOEO self test again, and look for a code 35. Ignore all other codes. If code 35 comes up, remove the jumper and replace the sensor.
The exhaust leak you had allowed extra air to enter the exhaust, and may have damaged the O2 sensors, but more than likely caused the ECM to learn a false setting. I would first try resetting the ECM, and then doing a relearn on it, and see if the O2 codes come back. If they do, you may have to replace them.
Take care,
~Chris
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