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I don't understand why you'd go back to stock? Assuming your stage II tune kept all systems in "ready" status, you should pass as no sniffer is required in CA on modern cars. As long as the smog computer can plug into your DME and think everything is "normal" you're good to go.
The only chance of you failing would be visual. Is that why you went back to stock? In my experience most techs don't really A) look that closely and/or B) don't really know what to look for - if they see two resonators under that car they assume cats.
On the other hand, going back to stock should not be resulting in your current issues, so not sure what's going on other than drive cycles. But, again, in my experience, it takes only a few short drives/miles to set everything back to normal. Certainly not days and hundreds of miles.
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