Often after a dental procedure, especially when an infection is present, you are at risk for developing a systemic infection such as endocarditis (heart) and meningitis (brain/spinal cord infection). You may have contracted meningitis in mild form, and/or have this infection now. A spinal tap is needed to diagnose this, but fever and headache are both symptoms of this problem. It is treated with antibiotics, and in mild form can take place at home. Also, you may have been exposed to another type of infection during the time that you had the root canal, and the infection may have caused damage to the central nervous system that has left you with chronic inflammation which might explain the fever (low grade only, as anything over 101F should be investigated by a doctor) and recurring headache. In any event, if nerve damage is the problem, possible steroid therapy and medications that work on the nervous system, such as Neurontin, may help. Please discuss these theories with your practitioner for their advice and further treatment. Feel better soon and hope this helps.