So sorry to hear you are in the same boat as me. I have very similar pain
and I have a positive ANA one time
and negative the next time
and the same on the RF. It sounds like, as in my case, it is RA or Lupus. For me it is gearing more to Lupus since my pain is mostly in my muscles and connective tissue, not my joints. I'm rather surprised he would start you on methotrexate without a diagnosis. How long have you had these issues? How long have you been on your meds?