Yeah, I too have a lot of reactions to things, and have a totally messed up GI tract. You might look into NutriGenomic testing to find out if your body has genetic predisposition to process things differently than the average person. I've got one genetic polymorphism that causes me to need far less of certain medications than the average person, and if I am given full strength doses, my body acts as if I've been totally overdosed because the enzymes necessary for detoxing these meds can't go as fast as "normal."
On the fillings, if you aren't having obvious outgassing from them, then don't bother. The exposure during removal will be far more than what you're getting by leaving them in. I was told by a biologic dentist that most people don't have trouble with them, that it is only certain folks who do, and those are the only folks he takes the fillings out for - everyone else he just recommends good dental care and just replace the ones that need replacing when they need it, and that's it (obviously, the replacement fillings would be non-mercury fillings).
If you have no confidence in the Naturopathic practitioner you see, then you should find someone else. I've "fired" many doctors and Naturopaths, including a world-reknown LLMD, because of lack of confidence in them.
Most Natural/Complementary medicine does not have much peer-reviewed, double-blinded, placebo controlled studies backing it, mostly because not many studies have been done. Doesn't mean the medicine doesn't work or isn't safe, just means the kind of info you seek on it is lacking especially in the USA. Other countries are starting to do more and more studies on this stuff, but it still is outnumbered by traditional Pharmaceutical research by quite a bit. But you can do your own research on this stuff if you want to: http://www.pubmed.gov/ is the best site to search for medical journal articles about
various things...this site ties in to the National Library of Medicine's archive of medical journal articles. Some of the article abstracts even have a link out to the actual article and sometimes they are available for free (most cost $15-30 or more per article).
Stephen Harod Buhner does list a number of studies in his book, "Healing Lyme" to support his herbal protocol for Lyme and coinfections, so you might find the type of info in his book that you seek.
Another thing you might look into is the ability of essential oils to heal the body. Dr. Jernigan uses essential oils in his Lyme protocol. There are studies listed on PubMed.gov about all sorts of research with essential oils that may interest you.
I hope this helps - take care,