ok re the low d3, that's easy, find a high potency vit d3 supplement, and make sure you balance it with calcium, magnesium and zinc. (zinc must also be balanced with copper).
i suspect with the low d3 that zinc could be low also. the possible hypothyroidism points that way also. could be worth looking into.
clarification re the magnesium test - is that a serum result in mg/dL? if so it converts to 0.82 mmol/L. you want to be 0.90 mmol/L at a minimum. which would be more like 2.2. even though it looks like a small increase, it can make a difference.
moving on (these next are not the kind of result i'm usually working with so bear with me re guesswork :S)
re hyperchloremia, can be comorbid w/ diabetes. there are links in research between neurologic disease, hyperchloremia, hypernatremia, and dehydration.
the high BUN, high Creatinine, and highish BUN-Cr ratio - possible link to GI bleeding.. related to H. pylori infection maybe??
[edited out cbc comments - in review they were stupid! lol]
my approach: no meds so far - just nutrient-dense anti-inflammatory whole foods, and supplements where needed
info: www.whfoods.com, www.nutritiondata.com