Is the pain in my jaw from muscles or from joints?

Consider. Consider the cause. Also, consider an evaluation by an osteopathic physician as there may be a manipulative technique which may help your symptoms and treat or augment your treatment.
Could be both. Tmj - or temperomandibularjoint pain - pain and tenderness at the hinge area of the jaw bone - is a syndrome of inflammation of the joint - but the muscles around the joint can get inflamed too. Treatments are guided by the cause - may need dental / or / ENT evaluation to decide best course of action.
Source of pain. Most pain comes from muscles, but joints can also become inflammed. Palpate the point of pain and if palpations cause the pain to change, then that is the probable source. Open and closing the jaw can cause either joint, muscle or both to become sore.
Touch your temples. The masseter muscle inserts(attaches) onto an area just above the temples on each side of you head. If there tenderness there, it's like to be a muscular problem.

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There . There are a number of single disorders that could tie all these symptoms together such as chronic fatigue syndrome or lupus. They could also be the result of several problems going on at the same time. This kind of situation usually requires working together with your doctor for a period of months to figure it out with multiple blood tests and perhaps some specialty consultations. Read more...
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Eliminate the cause. First go to your md to be sure there are no medical life threatening issues. If there are no medical problems then look into the bite, joints and muscles (TMJ) as that may be a likely cause. Whatever, you need to find the cause so you know how to treat the cause and not just medicate the effects. Read more...
A number of disorder. Wide array of symptoms. You should start with your PCP for a comprehensive work up. TMJ component likely but only to be treated in the overall context of your problem. Read more...