I would advise you to combine it with food. It wil be better absorbed since they are both fat-soluble vitamins. I never recommended my clients to divide the dosage over the day. You can take it all at once.
With levels of 29 mg/ml, I recommend my customers usually to start with 2000 IU (or 50 mcg) vitamin D daily for a few months and then measure their serum vitamin D. However…
Were you already taking vitamin D before your functional DX? If so, how much and how long? To get serum vitamin D concentration in the optimal zone, there are some personal differences as well.
For example, to keep my vitamin D levels in the optimal zone I personally need 4500 IU daily.
Here is a handout that I would recommend you to take a look at as well. It goes in depth on vitamin D and vitamin D supplementation.