Have you tried the ECU reset? Long shot, but if it is a "learn" issue then that may help. Here are the instructions from another thread:
Resetting the ECU back to OEM learn
I just recently replaced my oem airbox with another oem airbox. When I started my car it did exactly what yours was doing. My issue were the vacuum lines not being properly hooked up. It did throw a code though. I properly installed everything... reset the ECU and all is good for over 50 miles.