If you know of a "smog friendly" shop, they might overlook the intake and throttle body. I know I get problems with my JLP intake even though I've "modified" it to look like it's from SVT.

Depending on the tune, you might not pass the OBD 2 plug-in test because the readiness code for the drive cycle might be set.

Unless the tune has been specifically written to allow the drive cycle code to reset, it'll pop up and cause you to fail.

Did the owner delete any of the cats when he installed the exhaust?

Stewart