What kind of mods are you talking about? If you are talking about exhaust or intake and the likes you should be OK. You can do a few things, disconnect your battery cables for a few hours and reconnect, or do nothing. The ECU should reset itself. I got a few warning codes thrown at me for like a week *check engine light was on* but it went away, I figure it was the ecu adjusting to the better breathing. Hope that helps.
Like Jaysen said the only real ECU mod is Technosquare which is around $500 or so. It adjusts your cars ECU to the mods that you currently have, raises the rev limiter to 7200, and does away with your speed limiter.
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