Make sure you take D3, in a gel cap type form, not dry powder.

I think 4000IUs would be a good start, retest in 3-4 months.

There are no really complete testing instruments at regular doctors.
There is a Spectra Cell, alternative place. But at this point, the major issues are Vit D, B12, zinc, magnesium, etc.
She could do a B-50 on her own.

Many serum tests are not accurate. They will show very highs or very lows as warning, but many in between values don't reflect much. The Spectra Cell testing tests intracellular red blood cells.
http://www.spectracell.com/micronutr...itional-panel/

You know looking at that panel reminded me.... many gluten intolerant people do well on l-glutamine supplements. Much of the glutamine we eat stays right in the GI tract. Human breast milk is very high in glutamine, to develop the baby's GI tract to prepare it for solid foods. Some doctors give this OTC amino acid as a support for GI inflammation. It might work some for your daughter as well.

Cara should be along soon, with her more experienced opinions.
I will defer to her.