Well sweetie, if the vets told you no way was it Myco, they were lying. I've had a few rats come down with it, and it's awful. I was in no way implying you don't take the best care, I'm sorry if it sounded that way.
My guess is he had a multiple bacterial infection and that his poor little immune system got overwhelmed and the Myco just exploded and he couldn't get it back in check. I have no idea why the vet would tell you it couldn't be Myco. Every vet I've ever spoken to about rodents, when one experiences respiratory distress, that's the first thing they check for.
The rat you say is scratching herself raw, some stages of mites can be all but invisible, I know I've battled them. Try putting her in a small tub with paper towels in the bottom for 20 minutes, then take a flashlight and magnifying glass to the paper towels. You will be able to see it if there are tiny early stage mites. if you don't find any, my guess is she has indeed developed an allergy to something.
This is an interesting article I thought you might like to read.
http://www.afrma.org/med_scabs_diet.htm
I wish you the best with your ratties.
Gale