Your D3 levels are far too low for normal bodily functions.
You may also have thyroid, B12, calcium and other deficiencies resulting from low D3.
The doctor's recommendation for 1000 IU (international units)- I assume 1000 mg was a typo- is too low perhaps.
My feeling is that it might be too low of a dose, specially, should you have vitamin D3 resistance, which is a possibility if you have:
a. Low or high corisol
b. Low cholesterol
d. VDR polymorphism
Supplementing with 5000 IU of D3 in sublingual liquid drops, would be more in line with most health practioners recommendations and safe,
in cases like yours, but please do you own research & talk to your doctor, as my comments and suggestions are not intended to replace medical advice.
Start at 1000. Make sure you have no side effects like constipation. You can always up it to 2000. But 1000 should be okay. May take a few weeks-months, but that's not an unheard of dose.