Congrats you finally found a dentist who can do the right procedure. Regarding the toxin from Root Canal, there are 2 issues you need to solve. First is the infection issues (by the bacteria) which I think your holistic practitioner has addressed. Another issues is heavy metal toxicity. The material used to fill up the root canal may contained mercury, therefore you probably want to check whether your body have this heavy metal toxicity. One of the safe way to check is through hair mineral analysis (though there are some weaknesses for this test also). DO NOT take DMPS Challenge Test (risky for backfire, skewed result: http://www.dmpsbackfire.com/test/default.shtml).
Once you confirmed you have heavy metal toxicity, you need to make sure you take out all the mercury in your teeth before you do the detoxing (called chelation) for your body. Ask the dentist to check whether there is remaining mercury in your teeth (it could be not cleaned properly).
Regarding your immune system, you need to make sure your body is fit enough for the removal. Take it slowly one at a time so it won't give your body too many burden all of sudden (Since you have 5, you may want to do it one by one within proper range of time). Dr. Hal Huggins have good suggestion regarding time period for Amalgam removal (read his book It's All in your head), which I think can be applied for root canal removal as well (since it deals with body immune system).