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The reflash is the same no matter what you have on your car. As Jake mentioned, the ECU will "relearn" everything it needs to know once you install your new parts.
I'd get the reflash after headers, personally. The more complete bolt on package you have the better the Hondata tune will perform.
BTW, I have pretty much all of the bolt on parts besides an intake (I'm not getting one at this point until someone can design a reliable system that doesn't mess up the MAF values and actually increases performance over the stock setup without reducing performance down low) and am getting the reflash next week. I wanted to do a before and after dyno since I've never dyno'ed a car before and I wanted to give my car a chance to break in and get through the first oil change before hand.
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