I have had fibromyalgia for around 5 years, and have been trying to stay working. However I have recently had a severe reaction to a pain medication that has caused my condition to get worse, resulting in my job performance falling below set standards.

When It first happened (early november) My doctor dismissed my claims
that I was having a reaction, by stating I probably had the flu or something. I was given 2 epidurals, and recieved little relief from either and told by my doctor to go back to work.
I informed my doctor that I was having trouble keeping up on my job , and that I needed to be put on fmla untill I could recover (If I ever do recover)
the doctor agreed and said I would be covered for 6 weeks for treatment and office visits however She would not write me out on a temporary disability , even after numerous complaints and visits from myself explaining my condition had worsened, even though she would only vaguely aknowledge what i told her. And as a result I have stacked up enough write ups due to not meeting my standards on the job that I was terminated today.

Does anyone know If I might possibly have any legal recourse?

You don't at this point. Even if your doctor did not write you the note, your employer did not receive the necessary documentation from you. For future reference, what you should have done is go to a doctor for a second opinion.

I got a second opinion, and they said, that they did not want to write another Fmla (yet) with the other doctor already having one outstanding.

I am mostly curious about a medical malpractice issue, since it was the doctor who made my condition worse in the 1st place, then refused to properly treat or diagnose me.

You will probably want to talk to an attorney specializing in that area. This forum isn't the right place to learn about malpractice. Good luck.