Cyst & trying to conceive

A few years ago I didnt take the pill for about 3 weeks (wasn't trying to get pregnant, just hadn't been to the doc to get the script) but I was using other contraception for this time....anyway I woke up one morning with severe cramps which gradually got unbearable throughout the day and landed my in hospital. As soon as I got out of hospital I went and got the pill and 6 weeks later for my check up the cyst was gone.  

Now my husband and I are trying to get pregnant, and I am petrified I am going to get a cyst. I had a check up with my doc and got an ultrasound before i stopped the pill and no cysts he said ok to go off it...now i have not taken it for 3 weeks and have had lower abdominal pain, its just like minor period pain. And now I am getting some pain on my right ovary again. Its not anywhere near as bad as last time,but its a constant dull ache... but i dont know what to do as i cant go back on the pill I am trying to get pregnant? 

I thought the pain might be my body might be getting used to ovulating since I have been on the pill for 10 years it is a significant change,  maybe thats why i had some aches? Is this possible? I dont want the doc to tell me to go on the pill..is there any other hormones pills i can take to help the cyst but where i can still concieve? help