Welcome to MDC!
I think you need to focus on vitamin A as well, Nordic Natural is low in A, 20,000IU is recommended in addition to a diet with other sources of A. A high vitamin CLO will give you both D and A.
Everyone is different re: food intolerances, so it's hard to say for sure what an individual's gut will tolerate. Raw milk is very different than pasteurized, however, the proteins are easier to digest. But you would only know if you tried it. And goat is also much easier to digest than cow b/c the proteins and fats are smaller. My DS can only do goat milk yogurt/butter.
You can make your own nut butters from soaked nuts (see NT). The same issues apply to all whole grains, oatmeal, wheat, etc. The phytic acid has been shown to carry minerals out of body, unutilized. Soy contains some of the highest amounts as a matter of fact.
Chemical sources of vitamins are never as good as food. Bone broths are excellent source for these minerals. Also NT recommends KAL Dolomite powder for calcium.
And one final thing, if your DD has food intolerances thru BM that means you probably do too (leaky gut).
NT will be a fabulous read for you, do get it! Their other book, Eat Fat, Lose Fat
is also very good to be introduced to the Weston Price/traditional diet style of eating, but shorter (not just for weight loss).