If that's the case, then I'm fawked. Currently tearing down my truck for a turbo build. Have you *tried* another emissions location? That would be my first step. I really have trouble believing they so fundamentally changed the rules without any public notification. As I posted earlier, I have a lot of experience wrestling with Clean Air Colorado and there are ways around a failed emissions test, but seriously, I think this guy is yanking your chain or has not been properly trained (who at CAC has?)
:edit: for the record, my friend just recently registered a tube-frame race car that was built 100% from scratch in his own garage. Honda motor with a turbo, single cat and motorcycle style muffler, basically nothing was factory but the engine block (internals were changed). They didn't give him any trouble except for the stolen transmission, lol. This was like 6 months ago.
If CO is following CA standards, I'm taking my job, my family and my tax revenue to Wyoming.
You might not be hit the same issue I did. So, when you roll into a Colorado emissions station, one of the first things they do is open the Driver's side door and look for the bar code. They scan that, and that set's their computers to make, model, engine of what that bar code says your vehicle has. Then they pop the hood, they do a visual, there is usually a sticker on your hood that shows where the ERG, EVAP, and any other emissions controls systems are. The make sure they are there and then they plug into your ODB port. Their computer will pull codes, check your computer, make sure all the DTS sensors are working etc.
So in my case when I rolled in, they opened the hood and found that my engine didn't match the picture on the hood, and when they scanned my barcode and the computer was setup for a Toyota, but when the plugged into mine it came up as GM, that is what sparked the full on inspection.
And I am sorry... I guess I wasn't all that clear, if you have to go through a inspection that is where they are now holding us to CA/Federal emissions. For me, in the eyes of the emissions gods everything about my setup is evil. Again modifed motor, modified computer, modified exhaust (headers and my drivers side CAT was 4 inches too far back), etc, etc.
Also I decided to go big. I went with the 6.0L (LQ4) which was most commonly only in heavy duty trucks. They had it is some others, but my computer says 2002 Chevy Silverado HD. So they flagged me on having a heavy duty engine in a light duty truck.
Looking back on this, had I had to do it all over again, I would have just got a 5.3L and kept everything stock and I wouldn't have the issues that I am having. So I do think it is possible to keep doing cool things with cars in Colorado, I am just more aware that if having to go through a inspection process (which isn't common) that things need to be factory.