try backing off the d3 for a few days and see if just taking magnesium alone helps the pain. how much b-complex are you on?
what's your ferritin status like?
also, have you had your d3 levels checked? do you know how your absorption is?
i just found this highly unscientific looking resource, but very interesting. what makes me include it is that when i was zinc deficient i had pain behind my left eye. !!!
"T - Ache deep behind left eye may indicate a zinc deficiency."
and this is weird seeing i just asked you about ferritin:
"N - Ache of band like character around forehead may indicate anemia"