If our bodies are unable to process toxins, they become stored in our bodies - in organs, fat, bones, and even inside mitochondria, sapping energy production.
This is an extremely high level view of how we get rid of them... lots of details are involved, which I won't get into here:
We have several detox processes, which use different nutrients to process different toxins.
One of these is called methylation, which uses folate, B12, B2, B6, magnesium, ATP and some amino acids. If stuff successfully gets through this, we make glutathione, a very powerful antioxidant, which is tremendously helpful in defanging bad things.
Once the bad stuff gets caught by these processes, it needs to leave our bodies, generally in feces, urine, or sweat. If we can't get rid of them fast enough, they can get reabsorbed, making us sick.
Arbitrarily taking a bunch of B12, etc. can abruptly loosen up toxins, which can cause lots of symptoms, like the ones you're describing. This can make you very sick. I know, I've been there. You need to get rid of whatever got mobilized, then rejigged your methylation protocol to fit what your body needs.
Great that your urine heavy metal test was OK. However, was it provoked, with DMSA, DMPS, or EDTA? Each of these chelators only will pull certain metals out of you, so if the right chelator wasn't used, that metal may not show up on your test.
It's not just metals. There are all kinds of toxins and substances our bodies metabolize. Metals are just easy to measure. The estrogen you keep mentioning is one of these substances. You may have an issue with CYP1B1 or COMT which may affect how its metabolized.
Hopefully, your naturopath is a good one, and can sort out what's going on. He or she should be doing some of the things I mentioned above, as well as adjusting your B vitamins, and possibly offering IVs of curcumin and glutathione. And suggesting you do a 23andme test.
Good luck!