So I have assumed that the food pyramid and by association RDA's were reverse engineered from the made up assumptions of 9-11 whole grains ...blah blah blah. We now have the Kraken index for food that makes bacon the most nutritious. We know that HG's didn't exactly seek out kale. Question is what nutrients have the most scientfically backed RDAs (doesn't need to be the gov. ones, feel free to change the numbers based on what we know). I understand this is a tough one due to synergistic function and cofactors so where ratios are more telling go for it (example K2,D3 and calcium). Or, is it just a matter of a whole foods ancestral approach and everything will end up where it should be(lower carb reduces need for C)?
I believe Richard Nicoley had some interesting comparisons here: http://freetheanimal.com/2012/07/grains-vegetarians-vegans-and-nutritional-density.html and here: http://freetheanimal.com/2011/04/nutrition-density-challenge-fruit-vs-beef-liver.html.
He correctly points out that "super food" fruits aren't as nutritious as things like liver and you'd need a ton of them (with the added sugars) to get the same. This effectively proves that vegan diets are a failure, and at the same time that advertised superfoods aren't.
Not sure if it's what you're looking for, but you can also go here (or use the "site:nutritiondata.self.com" verb in google and ask questions like "food highest in K2") and get answers such as this page: http://nutritiondata.self.com/foods-000104000000000000000.html
To answer your 2nd question, personally, paleo isn't a historical re-enactment. We can take the best of what's modern and the best of what's ancestral and use them together for a more optimized life. We do know plenty of modern things are harmful (blue light at night, stress, lack of sleep, GMOs, artificial flavors, colors, preservatives, some natural versions of the same, plains salt vs salt that hasn't been stripped out of the other minerals, etc.)
Having done exhaustive reading on calcium for a research assignment, I can at least voice my opinion on that particular nutrient. This answer will be long, so skip to the conclusion if you want the gist.
The RDA for calcium is currently 1000 mg per day for an adult, rising for women after the age of 50, and men after the age of 70. This number comes after some serious debate.
One of the older studies I found studied the calcium needs of several Peruvian Prisoners. I was pretty surprised by how low the numbers were. The greatest calcium need (excluding the subject given calcium injections prior to the experiment) was only 377 mg per day, with an average slightly above 200 mg per day. Of note is the apparent fact that subjects were allowed outside in the prison yard during periods of full sunlight (making vitamin D go ↑). It's also briefly mentioned that subjects were drinking hard water, potentially providing magnesium.
Most studies have not found such low values. This study gave subjects 545 mg of calcium and many subjects went into negative calcium balance. Supplements, including vitamin D, were given to help avoid deficiencies. The average estimated calcium requirement was 644 mg, or 9.21 mg per kg of body weight. One of the studies lead authors, Harold Mitchell, famously performed numerous similar studies on calcium requirements, finding 9-10 mg/kg as a common requirement for non-elderly, non-menopausal adults (or about 600 mg for a 60kg person), although women seem to have greater calcium needs during pregnancy and lactation.
Of course, we know vitamin D increases calcium absorption and decreases calcium loss (5), so vitamin D status will have a big effect on calcium needs. That's pretty important, considering almost half of Americans might be vitamin D deficient (6,7). Magnesium appears important too, another nutrient a large number of people are deficient in. There are a lot of factors affecting calcium absorption, but I'd hate to forget to mention grain compounds (especially wheat bran) negatively affects calcium balance (12,13,14). Finally, vitamin K seems to help lower urinary calcium loses (17,18,19).
I can imagine it had to be hard to make the RDA for calcium. There have been hundreds of calcium balance studies done and huge ranges have been found, from about 200 mg, such as in Peruvian Prison study, to much higher numbers (4,5) that make 1000 mg seem like a good choice. The average is usually about 600-700 mg. Still, the RDA is supposed to be adequate for almost all people though, so the higher range is favored.
You asked about scientifically backed RDAs. I'd say there's a lot of science to back up 1000mg per day of calcium when you consider lots of of people are low in vitamin D, K, and magnesium levels and have inefficient calcium metabolism as a result (with grain consumption doing them no favors either) with many population studies reflecting this.
If, on the other hand, you're dealing with a population replete in such nutrients (perhaps avoiding whole grains too) then I think 1000 mg per day is much higher than needed, probably 700 mg or about 10mg per kg of body weight a day (assuming no abnormal health conditions) would be a safe value. Unfortunately, there just haven't been enough calcium balance studies in which vitamin D, K, and magnesium status were determined, so this is not definitive just yet.
What is your daily supplement regimen? 16 Answers
Replacing pills with real food 3 Answers
Supplementation Confusion 5 Answers