What Causes Irregular Menstruation, Headache, Nausea And Mild Fever?

I am a 20 year old female. I have irregular menses. But I think I may be pregnant. I haven't had my period and my primary doctor has me on Progesterone 200 mg for 10 days starting on day 16 of my cycle once I have my period. I had my period in November and took the medication December 2-11 and still haven't had a menses. My fiance and I have had unprotected sex during this time. For the past week or so I have been waking up with headache, nauseated, and a low grade fever. I have recently started having major lower back pains. I took a home test on Monday and it wad negative. Could it still be too early?