Rheumies will start one of the three meds, (Imuran, Cellcept, or MTX), based on symptoms. You say you are having "increased symptoms" and "are still dealing with flares" - that is why he is suggesting MTX.
I have never heard of using these based on blood work -- although it's a good idea. Lupus, being the strange and wonderful disease it is -- well, symptom activity often doesn't match up with what the blood work says, so they have to treat based on how our symptoms are doing. More symptoms, more treatment.
If you aren't around children, I wouldn't worry about
flu season. (I'm not around children, or very many people really, have never had a flu shot and haven't had the flu in many, many years.)
Lynnwood, Lupus & Sjogren's Moderator, Dx: 2002DIAGNOSING LUPUS & HW's LUPUS 101
"Life is far too important to be taken seriously." - Oscar Wilde