If you load the base tune back, put it back to stock in the tune, it will remove the fingerprint.
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Ill have to get some more info,im running a whipple 2.9, 123 cj maf, with a return style fuel system, ID10000 injectors, 373 gears.
Being a 2008 not sure how well the stock tune will run to get to the smog shop. I have some time since its reg is good till October.