Hi, ive noticed your question has remained unanswered, and i am sure there a many others who know more than me about clomid.
I think it is safe if used in low doses. See the thread in 'infertility' about seeing your RE, where someone mentions they are taking clomid and nursing. Also, i asked my doc yesterday and she said it was ok. I also checked dr Hale, and the only concern he mentioned was its impact on supply.
In your case though, since the problems with ovulation are related to nursing, i would look more at that. Its normal for your cycle to be the way it is while nursing. If you want to jump start your cycle without weaning, you can try to reduce nursing between 1am and 6 am, or leave a 6 hour gap between nursings. That helped me. You can also take vitB, maca, and vitex to regulate your cycle which are all safe while breastfeeding, and these may help you ovulate naturally.
You can also take soy isoflavones as a natural alternative to clomid.
Personally, i would not want to take soy or clomid for extended cycles whilst nursing. For me, i am only willing for 1 or 2 cycles.