I have been strict veg (no dairy) since 1998. In 2003, I went off the Pill, and within a few months was missing periods - and then having 2-month long periods. I was diagnosed with PCOS, a very odd case of PCOS - I had the cysts very clearly, and my periods were messed up but otherwise no symptoms at all, and no family history (and completely normal weight). I ended up addressing the "weird PCOS" with acupuncture and later naturopathic medicine, and never once was it recommended that soy might be a problem. I was not eating much soy at all when I got the diagnosis. My MD said I likely would have developed the problem much earlier if I had not been on the Pill (I take that with a grain of salt, she may or may not have been right).
About a year ago, I had a relapse of the period problem which I again treated with a short stint of acupuncture, and this year I've had a lot of trouble with pain in my fibrocystic breasts, plus shorter cycles. Although I do consume more soy now (tofu and soymilk), again neither I nor my doctors have drawn any connection there. For me, stress is the key: my body reacts very badly to severe stress. I've had everything from this supposed PCOS to breast lumps (benign but painful) to Pelvic Floor Disorder, and yet there is nothing in my physiology that should lend itself to any of these illnesses - and they are always atypical cases of the condition. Try as I might, I simply can't stay on top of the stress, and it makes me sick.
If you have not already, I highly recommend you see a licensed acupuncturist or OMD. Chinese medicine has a long, successful history of addressing female problems, including period problems, and without resorting to yanking out the plumbing.