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Well I think a lot of your woes are likely related to the liver. It looks like you were given a lot of standard process supplements to aid your digestion, address your thyroid, etc. which is pretty typical stuff. The standard process supplements make me think you did see a good naturopath at one point.
However I don’t see any unda homeopathics listed and this might be the best route to cleanse your liver if you are sensitive to the liver cleansing herbs such as milk thistle, dandelion, etc. I didn’t see this listed in your supplement list (liver cleansing stuff)…I think your liver needs to be cleansed because of all of your symptoms you mentioned while doing it. Its upsetting for me to see that these doctors didn’t do any liver cleansing.
Another part of your woes might be that you have become very very clean by doing the diet and battling the yeast, etc. and so now you have become more sensitive. Before you were a cesspool and so when you throw crap in a dirty cesspool, you don’t notice it. Now you are more like a clean swimming pool, so when you throw crap in the swimming pool you will notice it.
So I don’t think you are getting worse or anything, I think you are likely getting better.
However some kind of internal cycle is causing you not be well suddenly and a good naturopath would be able to figure it out. Based on your writing it sounds like you have a lot of anxiety/stress right now and I think the single most important thing you need to do is chill out and believe (or have faith) that things will get better. The stress releases all sorts of hormones, etc. that affect other cycles in the body, etc. and you need to reduce this. Once again there are specific homeopathics/supplements that can help with this, I just don’t know of them.
How bad are your symptoms when you eat foods that don’t agree with you? If you can tough it out while gaining better nutrition, this might be something worth considering. For instance, if the only symptom you get is brain fog after eating something…no need to worry about it imho. You’ll get better and don’t be so concerned about feeding the yeast, etc. The yeast fight might be something that will have to take a back seat for a bit while you address these other larger problems.
Are you taking a break from a lot of the supplements you listed? What are you taking currently?
One problem with molybdenum is it is a chelator agent and so it might cause problems and make you worse. Be very careful with it.
My final suggestion would be to consider looking into the methylation stuff.