I agree with your therapeutic regimen regarding this condition with the use of prednisone and folic acid.  I also agree that the methotrexate must be discontinued in order to produce a resolution of this patients’ skin problem. However, in my experience, this stomatitis may take a number of weeks to go away completely if a patient been on methotrexate, for an extended period of time, because the medication is stored within the liver and in fatty tissue.  Topically I have prescribed Lidex gel, which I find works extremely well in stomatitis conditions.  It can be applied t.i.d.  