I'm not sure. You'll have to research each nutrient individually - each nutrient is its own little research project.

I'm fairly confident that the optimum amount of vitamin D is probably much higher than the recommended dose. You can take that information into account as you see fit when judging the FDA recommended doses. My guess is that they generally tend to be too low. This might be ignorance, or it might be a precautionary measure to prevent supplement overdose - I'm not sure.

Being of the evolutionary-nutrition school of thought, I'd say the first place to look for deficiencies are the places where our ancestors would have gotten more than us even if we ate optimally given the resources we have. That means Vitamin D (we're sun deprived) Vitamin K2 (we grow up sterile so our gut flora do not synthesize enough) and Omega 3 (grain fed meat is lacking this).

Further deficiencies would probably depend on your individual diet and physiology. And by the way, if you are going to put lots of effort into being healthy, be sure to direct a good portion of that effort into optimizing exercise regimen and stress regulation, both of which are probably more important than diet.