If esr, crp, &c3, c4 were mostly normal during flares even prior to starting the methotrexate, why is methotrexate contolling all my flare symptoms & fatigue?

Treat the person: As a pathologist / lab doctor, I am always reminded and reminding people to look at the person, not the labs. They are very imperfect and indirect measures of what is really happening in your body, and are best used as monitors -- yet never as good as "how do you feel?".

See below: I am assuming that you have lupus because you are having C3 and C4 measured. Some lupus patients can have impressive synovitis or joint swelling by exam and an ultrasound or MRI can demonstrate it as well but labs would be normal. You did not mentioned if a dsdna level is being measured regularly. Unfortunately in lupus, we do have not have other tests available outside of a research to look fo.