Jinx, I am confused here. Do you have a root canal or not? A root canal is a procedure done by a dentist. It's where they remove the nerve of the tooth and everything and fill it in and seal it. It's done on a dying tooth. So in a sense you get to keep your tooth from this procedure, but it's not alive. And one must ask, at what cost? Unfortunately root canals are a breeding ground for infection/bacteria, and some are not done as well as others. This bacteria apparently is not always contained, but can become systemic and cause illness and many symptoms.

So that's why many biologic dentists refuse to do root canals, though now "apparently" there is another way of doing them that is more biocompatible and safe and some are now doing them because of this new procedure. I cannot vouch for it, I don't know enough about it. Check thse links out, it may answer a few questions. Showing two different materials used in root canals and which ones are preferable.
http://www.integrativedentalmedicine.com/RCTtox.html
http://www.integrativedentalmedicine.com/ocalexic.html

If you simply have teeth that have cavities and you are having problems/pain, then you may need to get the tooth removed completely. If you get a tooth removed (which is probably a healthier alternative to a root canal), then make sure you request a non vasoconstrictor, non epinephrine anaesthetic (because these products can interfere with blood flow to the area and contribute to deadening of teeth/cavitations and are also toxic). You will also want to make sure (ask) that they please remove the periodontal ligament as well as the tooth. You do not want that being left behind to sit there in the jaw when it's no longer of use. It just rots pretty much and intefers with healthy bone growth to the area. You have every right to request this, it's pretty basic stuff. Just make sure they don't pack the hole itself afterwards. Wadding is ok (just the stuff they put into your mouth to help with the bleeding). But putting actual stuff inside the hole itself? Probably not a good idea. Stitching it would be better. And make sure it's kept clean/sterile and simply eat as well as you can, take supplements, all to aid the bone growth to the area where the tooth has been removed.

I don't know enough about TMJ. But it's highly possible because mercury can apparently cause/contribute, as can other dental toxins. I had terrible problems with my jaw when I had braces. It was the toxicity of the metals in my mouth. IT was awful! That's when I dramatically drifted into ill health and never recovered from that moment onwards. But I did get to improve alot later on through diet. I'm suffering now with something else as you know, so the improvements are not what they were.