I think that it is a myth (or at least a common misunderstanding) that there is one TF diet. There are numerous diets from numerous cultures, and it is difficult to make our modern diets perfectly resemble the exact diet from a culture that lived a long time ago and far, far away. WAP took detailed notes, but he didn't make notes of exact amounts consumed of every little food and factor in all other lifestyle factors. For some things, especially through pollution of waters and depletion of soils, the foods we would eat today are not the same as they were then.
Nor do we know that any of the individual diets studied by WAP are a panacea for all people of all cultures, just that they worked well in the cultures they were used. It is clear that the people of individual cultures were using nutrient-rich diets based on the local foods available to them (and they tended to show an amazing ability to search out nutrient-rich foods in their own locales or make ways to travel or trade for them), but it is possible that they were also utilizing diets that worked well with their own genetics. This can be most clearly seen in the fact that some cultures relied heavily on milk and some did not use dairy at all, and the cultures that relied on milk tended to have a gene that allowed them to digest lactose better than the people from cultures that did not rely on milk.
There were some telling similarities that we can take to heart such as the fact that every culture that used grains/beans soaked/sprouted/fermented them and usually served them with an acid, consumed meat with some sort of regularity, and prized certain organ meats and broths.
OP, reading your post, I can only wonder, have you had your Vitamin D checked recently?