Count yourself lucky to have received a diagnosis, a lot of us never get that far with doctors. Having said that, 2 weeks of medication is rarely enough for chronic SIBO, which after 2 years of dealing with this, you most likely have. I think your treatment course would've been successful for a rapidly spreading, immediately symptomatic form of SIBO, such as the ones causing extreme bouts of diarrhea.
In your case, it's probably going to take 3 to 6 months of perfect dieting before you start seeing results, another few months to be "cured," and a lifetime of staying away from your trigger foods to beat this.
Only you can really tell if your naturopath is reliable (some are great! Most are quacks) but I agree that you probably have lactose intolerance - the egg white thing is most likely BS.