Hello, it may be the RA side of things, and the fact your MTX was lowered. Or the Prednisone, some of the symptoms you described are signs of a reaction??(I read the little insert once) My doc took me off of prednisone due to the weird aches, he told me taken over a length of time it does weaken mucsle/tendon attachment sites. Of course, don't take my word on it, you may want to ask your doc about it.
And yes, we all react to meds differently as well have the same symptoms but different.
Have you changed anything in your routine-more activity or less?
hope the new adjustment works out