Do you know if they do an OBD2 scan during the inspection process? In NC they do and if there are more than 1 readiness monitors in "not ready" status that is a fail. When you clear the check engine light all the monitors go to "not ready" until the drive cycle has been completed for each monitor which should re-trip the CE lamp. Why are the long tubes tripping the light? are there no O2 sensors mounted in the headers? Did you remove the cats and/or the after cat O2 sensors?
Curt