Just to double check I assume the doctor prescribed Vitamin D3 and NOT D2? It is wise to ask what Vitamin D level they are trying to reach and maintain. If they say an amount lower than 125 nmol/l ,that is not good. If they say anything from the 125-250nmol/l range, that will be great. Please read http://www.vitamindcouncil.org/about-vitamin-d/vitamin-d-and-other-vitamins-and-minerals/. It is very important! I would stick to the amount they told you to take for now. If you have PCOS you may need to keep your Vitamin D levels in the upper part of the range but really no one knows. (You will probably need a maintenance dosage of 4-5000iu or more.)
I think the doctor may not have addressed the PCOS because he/she feels the Vitamin D deficiency may be causing it and/or they want to see once your D levels are good then what issues are you left with. (Vitamin D deficiency does cause infertility and be implicated with PCOS.)
I believe you are the first person to inquire about Vitamin D and PCOS here on the Q and A forum and I do not remember anyone from the blog. So I have no feedback to give you. If you would be so kind though, it would be great if you could respond back and let us know how you are doing and what your status is? Remind us of your beginning Vitamin D level, how much you took and for how long each amount was taken? Present levels and how your PCOS is doing? That way we can help others in the future.