Ok, I'll take a stab at this.
First problem is visual. You might have a complete dumbass tech that doesn't recognize anything you have is aftermarket, a complete dumbass that thinks everything, even stock stuff, is aftermarket, or you could have a competent tech that can spot the "good" from the "bad". If you get the bad dumbass, leave, go to another shop, don't bother reasoning with the person. If you find a competent place, the visual problems you'll have are the adjustable fpr, the downpipe, possibly the maf, and, oh yeah, the lack of a cat.
When it comes to the sniffer, the cat is going to be the biggest issue by far. The next one will be the chip, what you have disables egr. If you have to go back to the stock maf, unfortunately that might actually hurt your numbers, but what are you going to do except find another shop that doesn't care. The rest of the stuff is fine minus the visual problems mentioned above.