Haven't had much time to read/post here recently, but this is something I've been thinking about, particularly as my DH has gained a fair bit of weight in the last several years of enjoying my TF cooking.

Based on my experience and reading, I don't think that the answer to "fine-tuning TF eating" generally lies in chasing down food intolerances. Nor does it lie in adding more of some magic ingredient (fermented foods, fats, sea salt, etc.). I think it would be more productive to go back to first principles, and consider the difference between "traditional foods" and "traditional diets."
Traditional foods are
specific food items that are grown and prepared much as they were in healthy, traditional cultures: pastured eggs, raw milk, soaked oatmeal, fermented vegetables, etc. This term also covers those foods that are widely recognized as "superfoods," such as liver.
Traditional diets are the
big picture of what/when/how people in these cultures would eat. How many meals did they have per day? Which foods were typically served at each meal, and in what proportions? How much animal vs. vegetable, raw vs. cooked, or fresh vs. preserved food did they eat? Did they practice any kind of fasting? Did children eat a different balance of foods from adults? How about pregnant and nursing mothers (again, talking about overall diet, not "superfoods")? What sort of diet was fed to the acutely ill, or to those recovering from illness?
From what I've read (and I seem to be amassing a small library of historical cookbooks and anthropological studies), it's a challenge to find well-substantiated answers to these kinds of questions. There are tidbits here and there, but overall, I still feel somewhat at a loss as to how to answer the big question: what to feed my family? To me, it seems like WAPF is largely ignoring this situation. TF is often presented as if we can just pick a selection of "traditional foods," and it will all work out fine. If it doesn't, we just have to add more superfoods. If THAT doesn't work, we're basically left with the conclusion that our ancestors' mistakes have left us and our children with inevitably poor health.
I very much disagree with this avenue of (non-)thinking. It seems much more likely to me that the true benefits of TF can only be realized when these foods are used in the context of a well-planned overall diet. Just as one example, mineral deficiencies are at the root of who knows how many health problems. Dr. Price would certain agree with this point (in fact, the reason he recommended foods such as butter and fish oil was because they contained "fat-soluble activators" which help us to process minerals -- not because he thought fat in itself was some kind of health tonic). Something to keep in mind about minerals, as others have mentioned, is that they have to be balanced: calcium with phosphorus, calcium with magnesium, sodium with potassium. What's more, our relative intake of carbohydrates, fats, and protein influences our need for specific minerals, and also influences our absorption and excretion of those minerals. Our bodies can balance this out to some extent, but this process in itself is nutritionally burdensome, requiring various vitamins, minerals, and enzymes to work properly. From this perspective, it seems as if blanket recommendations -- like eating more high-fat dairy, cutting back on grains, or adding plenty of salt to one's food -- could help some people, but actually make others' health worse, depending on their overall eating habits.
If we were somehow able to truly follow the typical diet of one of Price's healthy traditional cultures, we wouldn't have to think about these sorts of details. Since we're more or less all doing a cobbled-together version, though, I think we need to be more attentive to stuff like this. As far as what we can reasonably do about this, I can see two possible starting points (though there might be others):
1) Choose a traditional culture -- maybe one from your own family background, or maybe another that you consider to be especially worth emulating. Learn as much as you can about their recipes, typical meals, and seasonal eating patterns. Try to follow in their footsteps, making use of your TF knowledge and skills in obtaining and preparing these foods, to try and compensate for any details that might have been omitted from your sources.
OR
2) Use traditional foods in the context of a modern "scientific" diet plan, i.e. one that was developed by a nutritional researcher whose work you find convincing. This could be one of the great nutritionally-oriented physicians or dentists of Price's era (Page, Pottenger, Hawkins, Lee, or even Price himself), or one of the more recent advocates of low-carb, paleo, SCD, etc. Pick one that seems do-able, and that has a well established track record in improving people's long-term health. Give it a good try; follow the guidelines closely for several weeks or months, and see how you're feeling.
If it doesn't seem to be working, don't even bother trying to tweak it... just switch to another plan. Advice books for healthy eating are like buses. If it's not taking you where you want to go, just get off; another one will be along in a minute.

If you feel like you're getting really far off course, you might even cross the street and look for one that's going in the opposite direction: low vs. high fat, mostly veg vs. mostly animal, etc.
We've been doing pretty well with Dr. Kwasniewski's high fat/moderate protein/low carb plan. Of course, this and the other research-based diets don't claim to be "traditional" in the sense of replicating the practices of healthy traditional cultures (apart from paleo, which is basically a bunch of competing theories). But what are you gonna do?

One thing I like about many of the nutritionists from Price's era is that they based their plans on the ways Americans used to eat, before processed foods came on the scene. This gives us a cultural connection, and also keeps the social alienation to a minimum -- which is a big factor that's often neglected. Community is such an essential part of life, and shared meals are a HUGE part of that. (Especially this week, for Americans.

) This is a big, big drawback to Kwasniewski's diet, and it's the reason why I can't see putting my family on it in the long term.
This is turning into a hugely long post... sorry. I've started a thread to discuss the various "big picture" diet plans that were recommended by Dr. Price and his contemporaries (Page, Pottenger, Hawkins, etc.). I'm feeling called to try out their advice, starting with my children.