You might be correct. The smog tech may have been a little too extra cautious while inspecting your Honda Civic wagon because of the slight engine modifications. In either case, you'll be needing to prove the header is stock, or try another smog station and see if you get the same results. If the header does not look original and has no EO number, a smog station will not pass it. As for the catalytic converter, the best place to check is on CA ARB's (air resources board) website using their
aftermarket catalytic converter lookup table. You should be able to find all the specifications for the catalytic converter currently installed on your vehicle; assuming there on numbers on it. Find the CAT and match the engine class it was designed for. If you've got a match, take that print out with you to the smog station.