Goodness I'm sorry you are experiencing pain, and to answer your question yes some people with MS also have pain and in fact it can be quite similar to that of RA, weakness as well. The causes of pain and the target areas are different though, MS does not effect the joints at all. How long have you been on the methotrexate? Some of the medications for RA take months to work unfortunately. I remember when I was diagnosed with RA (my husband is the one with MS) and they put me on predisone I felt wonderful! When they weaned me off it though the pain came right back and it was months before I felt any relief from the Plaquenil.
I see you are taking prednisone at the moment. Do you think your mood swings could be from that? Prednisone is known for causing irritability and emotional upset in some people. Pain itself too can cause irritability problems. Just dealing with pain issues themselves can be hard, but add what might seem to be minor additional issues and tempers are likely to flare up. Also, not saying that you do, but if you have any issues with stress or depression that can also contribute to irritability and memory issues.
When do you go to see your rheumy next? It certainly is possible to have more than one issue going on at once, but if you are early in your treatment for RA it might just need more time. Best of luck and I hope you get some relief soon. If you have any further questions we'd be more than happy to help.