It sounds like you have balanced your methylation, since you were able to stop the methylation protocol.
How long did it take for the protocol to work for you? How did you realise what was going on and start to reduce the protocol - did you find you were "overmethylating"? Perhaps symptoms changed in some significant way which alerted you?
My apologies for this long winded post: tldr; my diet is the most important part of my protocol. My philosophy now is the less supplements the better and I hope one day to be able to stop all supplementation. My experience with B6 toxicity and neuropathy was terrifying. My journey to health has taken well over ten years.
Implementation of the protocol was sort of gradually implemented for me in fits and starts as I initially tried several things. My initial protocol after several years on SSRIs for depression, ocd, autistic type symptoms, panic and anxiety which didn't work well at all for me was a haphazard attempt at taking supplements based on books like the mood cure and online information etc. which was not very effective but did help somewhat. Getting off of SSRIs was an absolute nightmare and took several years of titrating the dose down.
I also tried several naturopaths and orthomolecular doctors which eventually led me to a gluten free and dairy free diet. I was also still using various supplements based on what I thought or felt was helping but I didn't really know what I was doing with supplements so it was mixed results. I was supplementing for copper toxicity and pyroluria which I seemed to have all the symptoms of.
The gluten free, dairy free diet was a huge improvement but I continued to have issues. I then got my genetics done with 23andMe and attempted to implement nutrigenomics per Yasko and others as well as high dose iodine for my thyroid. I have a lot of MTHFR (including homozygous 1298) and MTR, MTRR, CBS SNPS and many many others. I have a lot of genetic issues so this was another stepped improvement. Of course there seemed to be lots of detox reactions etc.
I'm in Canada so there are no good doctors here that specialize in MTHFR or nutrigenomics as the medical associations here don't permit doctors to prescribe vitamins or supplements for health conditions. This results in their licenses being revoked. So I wasn't getting tested and was on my own basically going by SNPs and symptoms. I used tools like Livewello and Nutrahacker. Acu-cell is a good reference that I use often:
https://acu-cell.com/
When I went to the full methylation protocol per Fredd and Richard it caused more noticeable improvements in mental health, energy, and improved thinking, motivation etc. but there were still problems that weren't being solved such as heart palpitations, joint issues, digestion issues continued anxiety, depression etc. I thought it might be detox etc. but I was taking huge doses of B12 and folate and was concerned about whether I was doing the right thing.
At some point after a couple of years on the full methylation protocol I implemented a low oxalate diet and had another big improvement and I was feeling better than any point in my life. I have SNPs around oxalate processing and I started having oxalate detox periods interspersed with feeling really great.
Then I implemented lithium. Fredd and others said they saw huge improvement and I had SNPS that indicated I might benefit from lithium. TCNII etc. so I was hoping I would be able to reduce my b12 and folate doses as it was getting very expensive.
Not long after that all hell broke loose and I was forced to stop everything as I was literally worried I was going to die. I thought I had done damage with the Lithium Orotate but I was taking only small doses. I was waking in the middle of the night in a full blown panic sweating, palpitations, tachycardia dizziness tingling etc. with a heart rate of well over 150 sometimes almost 200. I was having neuropathy and Lhermite's sign and was losing weight. I thought I was hyperthyroid and had that tested and an ultrasound but it all came back normal. I needed huge doses of copper (20 mg/day), potassium, sodium and magnesium and calcium just to stay sane and slow down my system. I had no idea what was happening because there is very little information out there about B6 toxicity. Then I realized based on this group
https://understandingb6toxicity.com/ that I had become extremely b6 toxic.
I realize now that once I had gone low oxalate my digestion had improved and my absorption of nutrients and supplements improved dramatically. Without the oxalate in my diet, my B6 dosage was way too high at 150 -200 mg of P5P per day and I had induced B6 toxicity which is Small Fiber Peripheral Neuropathy which had damaged my autonomic and sensory nerves. The high dose folate, magnesium, lithium, B2, molybdenum, zinc and high dose B6 had caused cellular level dehydration, copper and sodium deficiency which all contributed to the neuropathy. Now that I have stopped B6 and reduced all of my other supplements I am almost healed from the B6 toxicity. I don't take lithium anymore because I am able to absorb enough from food. I only supplement with iodine occasionally.
I'm at 13 months off of B6 supplement and most of my B6 toxicity symptoms are gone or minimal. I still need to supplement sodium due to blood volume issues but was able to re-start my b12, folate and carnitine and I am now doing quite well again. I have recently greatly reduced copper supplementation (huge relief!) and no longer need high dose magnesium or calcium.
I should stress though that most important piece of the puzzle for me is an incredibly strict ketogenic/paleo diet that is low oxalate, totally grain free, sugar free, alcohol free and basically zero processed foods of any kind. I avoid all chemicals and additives in food and I haven't touched any pharmaceutical product in almost a decade, not even aspirin. Obviously, vaccines are something I avoid like the plague.
I now only eat unprocessed meat, eggs, fresh vegetables and fruit and occasionally some low oxalate seeds like pumpkin or sunflower. I use beef tallow and olive oil for fats and keep my carbs low and my fat high. I try to eat as organically as possible. I also use daily coffee enemas for detoxification. Thanks to this diet I only need minimal supplementation and continue to experience improvements and I'm in the best health of my life. I am in better shape at 48 than most 25 year olds. I run 20-30 km per week, play hockey twice a week and lift weights several times per week. I haven't been sick in years. When my vaccinated family caught covid all I had with it was a mild headache for a few days. My diet is considered insane by most people but it is the cornerstone of my health protocol.