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Ask your tuner. Most quality tuners will be able to set the tune up properly. Ask them first, and make sure you have cleared the p1000 code before you go in. Also ask your tuner if they masked the p1000 code because they it will look like its cleared, but you will fail smog.
What if I put the stock tune in ,but left the intake on. Would the car throw any codes that way?
Maybe. It will probably run very poorly too. I wouldn't do it. The 05+ are picky as hell for the tune on the maf and any minor air flow changes will cause trouble.
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passing smog
