Re: Hormones affected

That is interesting. It seems like your immune-system is being stimulated, then shut down--a normal event, but reduced C3 sounds like whatever sparked the response did not take. This is very typical of parasitic infection. Sounds like some enzyme cleaved off a chain, in the initial stages of compliment activation.
You talk about co-infections, do you think you may have mycoplasma infection? aka lyme? Shroom

P.S. Does the breathing thing happen exactly at point of sleep state?