First I just want to apologize if my initial comment seemed snappy or condescending, I'm getting into a bad habit of writing long replies on my phone. This was a pretty decent fan theory, I just got hung up on some of the science.

While you're right that the exact cause of some autoimmune disorders is unknown, we do know how they work. The immune system works in to parts, the innate and the adaptive response. The innate is the immediate reaction to infection or damage, your cells release cytokines that attract white blood cells and make it easier for them to get to the site.This helps ward off pathogens, accelerate healing, and activate the more robust adaptive response. It works by breaking down pieces of foreign material, either from a pathogen or toxin, and using that to produce antibodies that will help eliminate it quicker and create lasting memory cells that will recognize the infection if it occurs again. Most autoimmune disorders are complications of the adaptive response where the body has produced memory cells that recognize parts of healthy cells and beings to attack them. While they can be very serious, they generally don't play out in the time scale presented in the movie or express the same immediate symptoms.

Prions are again another can of worms but the consensus is that they are the result of a misfolding of specific proteins found in neurological cells. There's no evidence that I'm aware of that they can form as the result of a pathogen. That nature paper you linked is both behind a pay-wall and, based on the abstract, concerned with how cells destroy broken proteins and how it might play into prion formation. Unless there has been a big shift in their understanding, prions occur spontaneously from healthy proteins in the brain and begin to generate themselves. This is most likely a genetic issue, but it is possible to become infected by eating the brains and spinal cords of infected animals (this is why you wanted to avoid eating beef from the U.K. in the early 2000's and why if you did you're not allowed to donate blood).

Thrax is most likely a virus similar to Ebola because he has a fairly lengthy incubation period, causes flu like symptoms, and finally "destroys" Frank's ability to regulate his bodily functions. Normally when you're dying from an infection, they symptoms that end up really killing you are caused by your body cranking up it's innate immune response to 11 trying to buy time for an adaptive solution to be made. High fever is super dangerous because while it helps slow down pathogen reproduction, it eventually kills your own cells. This is why a fever above 101F (38C) is so serious.

It's not really possible to put accurate labels on all of the events in the movie because actual infections don't have the same kind of dramatic narrative.

Keep up the fan theroy-ing though, this had the length and enthusiasm I subscribe for.