I have a bad case of TMJ, and I also have a very sore roof the the mouth. I cannot believe all the problems that arrive from TMJ....I am going next week for a mouth guard...I hope it helps.
It might be something neurological, but it might even be related to a sinus infection. If you have weakness, you might require an MRI for further evaluation. I would recommend you consult your physician. You might need an evaluation by an ENT as well.
I've seen an ENT recently. CT scan of sinus was clear. I do have a deviated septum, however. Also, I've had a slight dislocation of my jaw.
I would recommend you see your primary care physician for a full examination. He or she might want to order a CT of the face or sinuses for further evaluation of the problem and might want to refer you to an ENT for further evaluation and treatment.