If you keep the cats and your state doesn't do a visual check it won't make a difference. I run a rear mount turbo on my 07 f150 and it passes with flying colors. No visual here and I still have stock cats
I assume you are talking a Fox body. They might be also looking for the smog pipe lines that feed in around the cats. I have had them check for the EGR and smog pump before. It all boils down to the inspector and how much they care and how much they know. I got failed once for lack of an EGR even though it passed the sniffer with flying colors.
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