No specific diagnosis...scared to medicate

I have  been diagnoised with non specific autoimmune disease. In March I had a complete thyroidectomy due to a goiter and unusual cells in the numerous large nodes. The cells were granulomous. I have had for over a year acute iridocyclitis which is treated with prednisonal drops 2 times a day at this time, but never clears up completely. I tire easily and get sudden Flu like pain throughout my body, which I treat with ibruprofen. My RA doctor suggested I go on Methotrexate which I am reluctant to do because of side effects. He is leaning towards sarcoidosis, not enough symptoms he said to be lupus. I am a 56 yr old female and can put up with most of the issues except the eyesight when it gets bad. My eye doctor ups the drops when that happens. I have a positive ANA and dsDNA. I also believe my sinuses are affected by this disease as I do not get sinus infections until my eye drop dose goes to 2  drops a day. When at 3 drops a day I had no sinus infections. So is it ok to treat as I am or is there anything out there with less side effects? I want to feel better, but reading forums of people on Methotrexate they all complain of fatigue and stomach ailments. So why go on them unless my symptoms get worse?