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Amazed that they passed it without the stock air box and especially the CCV mod. Good for you, you got one over on tree hugger Kalifornia!
The inspection is not as stringent as on a car. The cars were manufactured with specific requirements that had to be met whereas our diesels were not. They are looking to make sure you have not made any gross modifications or alterations that would increase your smoke output. As long as you have your CCV going back to your intake and you have a filter on your intake you are going to be fine. They can't detect chips (only programmers) so hiding the **** and setting it to stock should be fine too.
Now if you are packing compoud turbos or giant stacks coming out of your bed then that might arouse their suspicion.
The techs are only trained to look at specific things (CCV, EGR, etc.) for their checks, but there are exceptions everywhere so I'm sure some shops are more lenient than others.
They plug into your OBD II port for the computer test so there's no cheating that. Especially since it's hooked directly to the DMV.
I think that a majority of the focus is the throttle snap test (smoke output) to make sure you aren't overpolluting and to take our money to offset some of the ridicuoulsy disgusting deficit the state has!