Actually, Becky, the low thryoid is more likely the culprit of all the
other things you have been asking about than the mtx is.  

Low thyroid may very well be because your RA is not well controlled yet
and like Alice said, it often comes along with other autoimmune
processes.  

Low thyroid (hypothyroid) can cause weight gain, moodiness, depression,
anxiety, hair loss, fatigue, a tendency to be cold all the time,
sometimes a feeling of fullness in your neck/throat, itchy skin, muscle
pain, etc. to name but just a few of the symptoms.   This sounds far
more plausible than all the things that you have been thinking were mtx
induced.  

Perhaps the thyroid condition was just beginning at the same time you
started the mtx?   Hopefully once you get your thyroid condition better
controlled, you should notice an improvement in a lot of the things you
have been struggling with.

Good luck!

Donna G