Switching the aftermarket air intake unit you previously had installed on your Honda Civic to the original air intake box would have made a minimal difference on the smog check emission results, assuming the aftermarket air cleaner was identical in connections to your Honda's original air intake.
The PCV being connected is where the emission result difference comes into play. Depending on how the PCV was originally NOT connected, ie. missing and allowing unmetered air in to the intake manifold or missing and intake manifold plugged, or simply broken and allowing unmetered air into the intake manifold, the emission results would have changed on the subsequent smog check.
At this point it is necessary to inspect your Honda Civic's smog check results with the PCV connected and functioning. It is possible your Civic has other emission problem(s) which were masked by the improper operation of the PCV valve/system.
In our expert opinion, the smog station more than likely was not responsible for your Honda Civic's smog check failure. It is quite common for a vehicle to fail the smog test after a known smog fault is corrected; requiring further diagnosis down the flow chart.
Should you like to use our Online VIR Diagnosis System we can look further into why your Honda Civic failed the smog test. It will be important to know the smog check results of the CO, HC, and NOx emissions.
