You need to get tested for MTHFR, of you haven’t already. Ask your health care practitioner to order a genetic test to see if you are heterozygous or homozygous for the MTHFR C677t mutation, or if you are homozygous for the MTHFR A1298C mutation. If you are, you may be having severe methylation issues. My son had many of the same symptoms you describe (with the exception of the cracking joints and lumps in breasts) and he has been able to improve dramatically after discovering he was homozygous for one of these mutations, and then getting treatment. Good luck!