My first thought, upon reading the title and the first bit, is foremilk/hindmilk imbalance. I still think that's a very possible problem if the green poop has been a problem for a while. I think it would be well worth taking steps to correct a possible foremilk/hindmilk imbalance (block feeding, massaging the breast to encourage the milk ejection reflex aka letdown earlier, pumping on the side baby is not nursing on to encourage the MER, etc.). Oversupply is also a possibility.
It does sound like the vit D drops may have had an additional effect. IMO, I wouldn't bother with the drops. For one, your baby is under 6 months and unless your baby has been tested and shown to have low vit D levels, I would advise against direct oral supplements. ANYTHING a baby gets besides breastmilk affects their gut negatively, not just solids. This could be the case here (and you cannot always see the signs, EVERYTHING negatively affects their guts, it's just that it is sometimes obvious and other times is not at all). Instead, if it is a concern for you, I would advise you to take vit D supplements yourself. Vit D has been shown to increase in milk levels if mother increases her own intake (via vit D rich foods and/or supplements). This way your baby will get increased vit D but without the harm to her gut.