The positive ANA is a clue - a component - that goes along with your symptoms. It isn't an answer in itself. It may take awhile to pull everything into focus. You need a good rheumy, who follows you regularly, repeating tests to see if things are changing.
Personally, I would look for another primary care doc as well. I remember being in similar shoes 3 years ago. It is very frustrating to feel so awful and not have answers. Once I started treatment with Plaquenil, things got much better.
My diagnosis is still UCTD (Undifferentiated Connective Tissue Disease) as my labs don't confirm anything more specific, just the consistent and fairly high ANA along with the symptoms. I tried going off the Plaquenil and everything returned, so we know that is therapeutic for me.
Hang in there, and don't give up. Incidentally, I also have a celiac diagnosis, which came after starting on the Plaquenil. You said you felt much better for a time on the clean diet - you might want to investigate a possible connection there. Untreated celiac can cause many similar symptoms. Just a thought.
Good luck, and keep posting.