As long as the check engine light isn't on you should be fine. I know people with long tube headers who have gotten through with no issues. Thankfully they don't do a visual inspection. They just hook up to the OBDII port and check for codes.
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~Rob 
-DD Air Guide, Stillen G3 CAIs, 63mm Throttle Bodies, Motordyne M370, Berk HFCs, FI TDX CBE (non-res, CF), Sprint booster v3, Ecutek Dyno Tuned, and the list goes on...
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