Yes, I always feel fluey and have been like this since starting MTX 3 years ago. I have sinus problems and headaches from it. Recently I have started taking an antihistamine which does help - but I cant take them everday. someone told me to drink lots of fluids and that helps with the headache.
I hate how the meds we take can be worse than the disease itself.
I would ask your Rheumy to maybe drop your dosage to a more comfortable level - if not a whole new med that may not give you such bad side-effects.
You may be lucky and this will go away after a few months too - maybe give it a couple of months to see if it settles for you.
I am sorry you are suffering so much.
Keep us posted as to how you are going.