I think food is the largest amount of chemicals that we ingest. So food can have the most effect on our health. Unfortunately, doing long term double blinded clinical trials on each and every food item is prohibitively expensive, so the mainstream ignores food as having much effect on health. So all the nutritional information that we receive is through epidemiological (aka observational) studies. Unfortunately, epidemiological are known to be done in the cheapest possible way, which results in lots of bad data. The reason why they are used is that it is easier to get whatever information you want from them. Great for getting grants which are profitable and vast possibilities of generating papers. Even if epidemiological studies are done with great care they should only be used to generate hypothesis, which need to be tested with mice studies and finally with long term double blinded clinical trials before finally accepting it as a truth.
The other problem with individuals is that the response of each person to these chemicals is highly individual. In the case of medicines, there is an entity that wants positive outcomes, and many researchers will do indulge in malpractices to get the expected outcome. So its a very problematic condition in the medical world. Even animal studies tailor their studies to get pre expected results with 2-3 years, so they start with special mice and use special diets.
It is a hard problem for the person trying to determine what is good for them and what is not. The best option is to do your own n=1 study, and use those results. Of-course with these studies sometimes you end up with local maxima, which is not anywhere the real maxima.
Now the above would seem to be an intractable problem. But then you can employ some heuristics to select experiments that should be done to reach a better outcome than random testing. For me that heuristic is the Palaeolithic Principle. Generally our bodies have evolved over time, and it has evolved under selection pressure created by environment as well as diet (due to food availability). The last time humans moved out of Africa (where our ancestors evolved from our immediate predecessors), was around 70,000years ago. The adaptations at this point will be common to all people, but adaptations after this point may or may not be universal. So foods at this point should be good for us. The only trouble is that all the foods that we use today are highly evolved (artificially selected by humans) from those times. So we don't have the same foods, but the classes of foods should be generally similar. Also we can observe what other primitive societies eat, to determine what would be good for us.
Humans have been cooking for at least 200,000 years ago, so cooked food is a required part of the diet.
What we do know is that all these primitive societies eat a lot of fiber and FODMAPS. Much much more than what we eat today. They eat anywhere around 150gms, while we barely reach 25gm per day. This is a very big difference. We do need to note here that there are African peoples who have evolved separately from us, that have slightly bigger colon, which allows them to digest even more fiber. The 150gm number is from Polynesians.
Another is that all of these societies eat meat, there are no vegan or even vegetarian societies. The actual amount varies a lot, from the Inuits (which eat mostly meat, and have a peculiar adaptation to high protein consumption for heat production) to the Polynesians that eat very little meat/fish.
The majority of fiber was obtained from root vegetables, not from fruits or above ground vegetables or leaves. In fact eating leaf is not that common in traditional societies. There maybe a problem with trying to increase fiber without a healthy gut flora, so it might be a good idea to supplement with some good probiotic, while increasing fiber and FODMAPS. Elixa is a very interesting probiotic.
The above is just an example of how you would explore this heuristic. The benefit is that you can also think of this heuristic for other parts of a lifestyle. Some examples below.
1) Exercise - Exercise in those times was basically hunting or gathering, or sometimes trying to save your life. They used to walk a lot, and at a fairly brisk speeds. Humans also are known to be able to hunt down deer just by outrunning them with their superior stamina. Look for persistence hunting. That would give you a clue what kind of exercises will be best for us.
2) Meal times - Humans had their biggest meal around sunset. We are talking about Africa only :-). They did not eat all the time. Breakfast would probably happen with leftovers and rest of the day it would be small snacks subject to availability.
3) Sleep - They would sleep not long after sunset, and wake up with sunrise.
4) Probiotics - Humans were not very clean they got dirt on all the foods they ate, and so got micro-organisms in their bodies all through their lives. Contrary to popular belief humans did not die that easily. The majority of deaths happened for children pre-puberty. If somebody reached adult hood they were likely to reach old age, barring accidents, or epidemics. The frequent reaching of old age was the reason why women have menopause. So the micro-organisms must have caused children to die but adults became resistant to most diseases and were able to live long lives. Also the healthful micro-organisms stayed in the gut and provided a lot of health benefits. The present population has very depleted gut flora, and this is possibly the major reason for some types of health problems, particularly related to auto-immune diseases. Also these may have a bearing on modern diseases of civilization, aka heart disease, diabetes and cancer. These are mostly non-existent in populations living traditional lives. It could be that the people who survived to adult hood were more resistant to these diseases as well.
If we try to tailor our lifestyle around such heuristics they will tend to work for us. You can then try to extend the framework to decide on what to do for adaptations that you might have due to your ancestors. The important part of ancestral diets is the way they combine or prepare a food. That method has a lot of impact on its healthfulness, as food tends to work best when they are not eaten in isolation, but in combinations. But be aware local cuisine of a society can change drastically within 50 years. So you have to be sure that the food items you are looking at are really old. In any case anything that has been there only been there less than 50 years is probably suspect.
For example wheat is traditionally cooked after fermenting it with yeast or yogurt. Also the wheat used to be freshly milled, and not to a very fine consistency. Then it was sieved to remove the husk. Lastly all societies eating wheat also ate milk (obviously raw in those days). The last is a pretty interesting observation. Populations that don't eat wheat, are mostly not able to digest milk (lactose intolerance). My expectation is that there is something in wheat that required raw milk, and that adaptation was forced, when people started eating wheat. Another factor is that only Europeans who eat a lot of wheat have the kind of the peculiar white skin. No other people have this feature. Not the Inuits that never get sun or the middle eastern people who do get a lot of sun. I think it has to do with the combined effect of the Vitamin D depletion capacity of whole wheat and lack of sun all year round.
To conclude everybody must assess their lifestyle and determine ways to improve on it. How to do it is a hard task, as modern science gives very confusing signals regarding diet. The only possibility is to use a framework that allows one to experiment on themselves and come out with possible results that would benefit them greatly.