Did the doctor ever tell you what your progesterone level was after he did blood tests? Are you seeing a OBGYN or reproductive endocrinologist (RE)? I just switched to a RE, and he is very helpful and knowledgeable to my situation. I think I am in a similar situation as you.
I also have very low progesterone levels. My levels were at 0.25 before I started clomid, and now after the first month of clomid, they have gone up to 2.1....this still is not good b/c it is best for your level to be above 18. My doctor says that I am not ovulating, even on 100 mg of clomid.
There are two different kinds of progesterone supplements that your doctor may give you. I started on prometrium, which made me dizzy and tired. Now I am on provera, which I have no side effects from. Medications are different for everyone, your doctor will just have to figure out what works for you. Also, my only side affect of clomid has been mood swings.
Also, ovulation predictor kits did not work for me, b/c I am not ovulating. Does your doctor think you are ovulating? My low progesterone levels are causing me not to ovulate.
Like I said, I'm only on my first month of all of this, so I am fairly new too. Good luck to you, and if you have any questions, please let me know. It can be really difficult to deal with all of this new stuff!!