I have not improved further, but made the following observations during the summer:
*A too high Vitamin D appears to be bad and it cannot be offset by a lower calcium intake.
*Surprisingly, I seem to be improving somewhat when I eat 1 teaspoon of ground mustard seed with every meal. The more pungent yellow variety seems to work better than the milder brown seeds.
*Nitrate seems to be mainly a problem when it is combined with other problematic foods, especially monounsaturated fat, but also fat in general, fructose, possibly pectin or acid. For example, I can tolerate this meak surprisingly well: 6 oz of wholegrain spaghetti, 5 oz of kale (nitrate!), on sliced carrot (nitrate!), a few florets of cauliflower (some nitrate), a tablespoon of concentrated tomato puree, 300ml of water, all pressure cooked for a few minutes until the pasta is soft. Separately a teaspoon of ground mustart seeds. I used to think this would never work because of the nitrate, but because it has low fat, low sugar, low acid and low pectin, it seems to be ok. What's very interesting is that this meal isn't even so low in lysine. So I think it's the combination that matters.
*Mushrooms and nutritional yeast work quite ok if they are not combined with fructose, acid, pectin or a lot of fat, especially monounsaturated.
*I probably have to have a closer look at pectin, because its main sources, e.g., onions and apples, are worse. For instance, adding a large onion seems to make the meal mentioned above much worse and apples and oranges (both high in pectin) appear to make me worse than other fruit. Also, undercooked potatos in which the pectin isn't broken down completely are very problematic, while thoroughly cooked potatos are much less problematic. I think the pectin has to be combined with protein (probably lysine), fat and/or nitrate to have its worst effect. I will soon try to see if an onion soup that contains basically just onions makes me worse.
*Glucosinulates in cabbage family vegetables (brassicaceae) do NOT appear to be the culprit, because adding ground raw mustard seeds (which leads to the creation of glucosinolates like sulforaphane) to cooked cabbage veggies does NOT make me worse. I'm not yet sure about organosulfur compounds in allium family vegetables (onions, garlic, leek...).
*Caffeine seems to be bad, but I seem to be able to tolerate some vegan hot chocolate (coco contains caffeine) every once in a while. Same with cinnamon.