The starting dose is 1,000 IU per 25lb body weight, then retest in 6 weeks and adjust the dose accordingly. Ideal range is at least 50mg/dl, or more.
Low vitamin D levels will stop you absorbing magnesium properly as it does calcium. And lack of magnesium can cause kidney stones. I recommend at least 600mg as any organic form, these end in '-ate', like citrate or glycinate.
It's highly likely she's deficient in vitamin A and K as well as the fat-soluble vitamins all work together. Eating liver once or twice a week provides plenty of vitamin A; beta-carotene will not work as 45% of the population can't convert beta-carotene to retinol at all and the rest do so very poorly. Alternatively cod liver oil is also very rich in retinol, Green Pastures brand is best, as most others are rancid before they hit the shelves. They also do one will butter oil which will contain vitamin K2. Or you can supplement K2, best form as MK-4, 1mg is a good dose. Thorne does K2 drops and also D3/K2 drops (http://www.thorne.com/Products/Cardiovascular-Support/Circulatory_Health/prd~KD500.jsp). These drops have an ideal ratio of D3 to K2.