As I recall the chip needs to be re-calibrated for headers. His standard chip reduces fuel by 3% since the stock chip is rich at 6%. However for headers that would be where he returns it to.
This is one of the few things Mark does that I am not crazy about in that you need to pay extra to return the chip to 6% after he reduced it to 3%. He also has a "anti backfire" calibration for headers which he charges more for on top of his prices.
I think he should have at least a few chips for a header mod instead of having to re-calibrate and charge extra for it.