AZFX4 - I've been watching this thread, but haven't really had anything to say, so I stayed out of it.
However, until you talk to Bill, I would strongly advise that you DO NOT return to the Level 0 Stock tune. That is guaranteed to set your P1000 code and that in itself will cause you to fail.
I'm somewhat puzzled by the symptoms you have though. I'm reasonably certain nothing in Bill's tunes effects the Evap System. So, I wonder if there's possibly a sensor failure in that circuit? The EGR though is a whole different matter. I WOULD expect Bill's tunes to interact with EGR. I suppose though, there can be a sensor failure in the EGR circuit too. I have no electrical information on your model year truck, so I'm just guessing.
Now, it's possible if you reset to Level 0 and then reloaded your tune, the problems would go away. (But please don't do that unless Bill says to do so.)
One thing that would be safe is to check for codes. Have you done that? And, if you find any, try to clear them.
Beyond this bit of pretty fuzzy advice, I've nothing brilliant to offer. Yours is the FIRST truck I've heard of failing an emissions check while being tuned.
And, 88, I doubt the "cord at the shop is bad". Here in Arizona, inspection stations are licensed facilities with several entrance bays. And, they are not affiliated with any "repair" facilities. Unless he used the same bay, he'd be getting a different monitor. And, I doubt a bay would go belly up on just his truck but think everyone else's is fine. I DO think there's a problem, but have no clue how to fix it.
- Jack