I didn't realize it was old thread until I read your post!

I passed smog just a couple of weeks ago, with a Magnaflow exhaust on the car. My daily driver is fairly heavily modded but nobody ever said anything about the exhaust on it, and nobody ever said anything about the aftermarket exhaust on my Miata, either. But intakes? Yeah, they hate 'em here in Cali. I've got custom hard pipes on the turbo plumbing of my daily driver, plus the exhaust, and thee places wouldn't even talk to me after opening the hood on that car. I finally found a place that would smog it (once they verified I didn't work for the State) and in the end it ran so clean the guy told me I probably couldn't kill myself in the garage with the darn thing it was so clean. Heck, what came out the tail pipes is probably lower in many pollutants that what entered the engine.

I'm sure the reason there's no issue with aftermarket exhausts here in Cali is because, especially with a cat-back system, you've downstream from everything related to possible emissions out put - from any intake sensors, the O2 sensors, cats, etc.