I am not an expert but I can relate, I also have Hashimoto's/hypothyroidism and my endocrinologist just did a blood test on Friday to check for PCOS, she is checking to see if I am insulin resistant and with my symptoms, tired, low progesterone, history of ovarian cyst. I am just glad she is getting the ball moving! I mc in December and it took 4 months to get pregnant and now we aren't having any luck at all. I have 2 boys but we would really love another, I know how you feel and it is very hard to understand.. Ask your endo to run more tests on you to see if they can find something, it might be something really simple that your ob/gyn just isn't looking for.. Good luck!
I would suggest trying acupuncture and herbal medicine. You should go to a reputable acupuncturist/hebal medicine practioner. They may be able to help you alone or in conjunction with western fertility treatment. Take a look at my website to get an idea of what acupuncture and herbal medicine is: www.integrativefertilitymd.com
Not knowing is the most frustrating part! Good Luck to you also.