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I would not worry about your aftermarket lights, they had nothing to do with your engine malfunction. The dealer is not going to give you a hard time unless you had a failure that was directly linked to your modifications ( bulb warnings, etc.). Now, if you had a supercharger installed then you would be raising some red flags.
And to answer your other question, yes, the fault codes will be stored in the DME, DSC and other modules so the technician can find out what the cause was. Really does sound like the idle valve issue. Good luck,
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