Shortness of breath, fever and burning in my entire abdomen. .. Worse by smoking and eating. Pain also in head neck and back. .. History of ovarian cysts and endometriosis and ideas?

See a doctor. You need to be seen face to face, have a detailed history and physical exam and perhaps some lab tests and imaging studies. This cannot and should not be diagnosed over the internet. You sound quite ill and should do this asap. Hope this will be self-limiting and you will be better soon.
Ovarian cysts. It is possible that you have an infected cyst that may have gotten into your blood stream and is responsible for all your symptomotology.I would see your doctor or to the er asap to get checked out.