Which intake is it? AEM, INJEN, or HKS?
The CEL is there from your intake. The problem is the air metering. You don't need a tune for a catback, or lightweight flywheel.
The cost of changing your intake to a K&N Typhoon SRI, or SPT SRI and selling the one you have on now is going to probably be less than the cost of a tune. Most tunes are approximately $300.00 The K&N SRI and SPT SRI don't have any metering issues like most others do. (the APS, and COBB as well, but I don't care for either)
If the lightweight flywheel weighs under 13lbs then you're not getting rid of that check engine light. Your car thinks it's misfiring because the engine speed is too quick. The ACT Streetlight flywheel is designed with that CEL issue in mind.
Back to the tuner thing. HBSpeed is well regarded, as well as Harman Motive. The latter quit tuning for a while, I don't know if they're back in that business or not though.
If you REALLY want a tune... at minimum get a downpipe first. Make the tune worthwhile!!