Thanks for your query.Based on the facts that you have posted it appears that you have problem of pain in epididymis
since a long time
You are trying for conception however your partner has problems in her menstrual cycle indicating that she may not have ovulation (Formation of egg).
Get her checked by a qualified Gynaecologist and for further treatment to regulate her menstrual cycle.
You have to get your semen analysis
done to know the quality and quantity of sperms for effective for fertilization.