JMM,
Welcome to the board
I would have an MRI of the TM Joints done by my doctor to see if there is any actually joint damage. I am not sure how they determine if TMJD is more muscular related as I didn't have that type. Hopefully someone here can offer help on how that is diagnosed.
I would look into it a bit more before going into and paying for physical therapy. You may need other treatment first or in conjuction with the Physical therapy. Don't rush into anything as the wrong treatment can cause more damage. Seek some more answers first.
About the yeast infections some people get them from taking certain antibiotics. Check that out and see if there is a connection there. Your gyno may have some more or better advice for you on that. I would see them.
Good luck! I hope you find the answers you need to get proper treatment.
Autumn