I've adopted a two-pronged approach:

1. What did my ancestors eat?
2. What does the science say?

The first approach involves tracing my lineage to figure out what they ate. My family is Russian and Ukrainian, so the idea is to figure out what the most traditional foods are. I assume my genetics is going to be optimized for that environment. For me this means more cabbage and more buckwheat. However, though potatoes are popular in Russian cooking, they're a modern addition.

The second approach is to figure out what vitamins, minerals, etc my body needs. Essentially, you treat the body like an old-school Ford factory where raw materials come in one end and the end product (healthy cells) comes out the other. Another way to think about this is that if I had to put a feeding tube into by blood system, what does modern science say the mix of ingredients should be? Yet another thought experiment: take a healthy person and figure out what elements from the periodic table of elements exist in the body and in what proportion. If a healthy body contains magnesium but it's not in your diet, clearly you'd see some health consequences from this.

Finally, synthesize the two approaches. For example, if you have darker skin, you'll probably need more Vitamin D if you live up North. It may also be useful to pay special attention to "weird" foods of your ancestors since they may contain a beneficial nutritional profile that filled a gap. Buckwheat was one such food for me. It's packed with nutrients, but eating the same foods may not be enough. The same food grown in different geographies will have different nutritional profiles. I know rice can have varying composition depending on where it's from. In theory, you can become nutritionally deficient even if you eat the same foods as your ancestors and it could come down to soil composition.

The hybrid approach may seem complex, but it's simple to start since you can start eating what your ancestors ate and then take a lab test for nutritional deficiency to see if you're lacking in anything. The benefit of the hybrid approach is that they balance out each other's weaknesses. Science can't say anything about a chemical it hasn't studied. Even if it's studied, the science may only make claims about what's been observed or what can be inferred based on known mechanics. Traditional foods tell you what your genetics are likely adapted to. This may include chemical soups that science hasn't gotten to yet. However, just because your ancestors ate a certain way doesn't mean it was optimal for them. Finding the perfect diet is a back and forth between science and tradition.