Did you change anything else in the Intake tract? either pull and change both plugs, or give them ample time to dry out, air out the cylinders. then run it with and without the new and old filter to see the changes.
If the new filter provided much better airflow this would tend to lean out the mixture, which from the factory was already on the lean side. If it gets too lean then you will get a misfire, backfire popping that you described. You will probably have to have the ECM remapped to match the new airflow from the intake, and you will see a much improved ridability when compared to the stock programming.
Later