Positive today for mrsa in my nose very sore throat chronic cough headache puffy sore scalp can this all be related to the spread of untreated mrsa?

Not likely: Mrsa colonization by itself causes no problems, but puts you at risk for invasive disease if you have major events, like surgery. Mrsa is an aggressive pathogen, so it isn't likely the cause of chronic sore throats or headaches. Unnecessary treatment of MRSA colonization leads to other problems like increased resistance to other antibiotics as well.