I just lost my health insurance and I cannot afford to go to the doctors or the emergency room. So here I go. For the past 3 days I have had a minor fever, between 99 and 101, along with severe muscle aches. Along with this I have had a headache. Now while I am sleeping the pain is ridiculously painful to the point where I have a hard time sleeping but when I wake up in the morning I feel much better, except for a minor backache. But later on in the day around 3 or 4 everything comes back, including the fever. Now last Tuesday I went to the emergency room for a huge bubble on my arm and they are treating me for a staff infection. I will finish the medicine today. The antibiotics they gave me are Keflex and Bactrim DS 800-160. I didn't know if I could be feeling this way because of side effects to the antibiotics.

Sounds as though you may have a flu. Treat the symptoms. The antibiotics will not help the flu as it is a virus and has to run its course.