Someone please correct me if I'm wrong:
Generally when you add an intake there's the chance you could run lean. Since you have an '07 (same as me) it's more than likely not an issue. Your custom tunes took advantage of the increased airflow, though, and compensated for it if even in the slightest.
If you take it off there's a chance it could go the other way and run a little rich, but personally I wouldn't worry about it. Check up with Bill at the PHP Forums to get a solid answer from the guy that wrote your tunes.
