What Causes Fever With Headaches And Neck Discomfort?

I am 28, a grad student. I have a fever (99-100) that is intermittent (every 3-5 hours) and presents with a serious headache (7 out of 10 pain), and neck discomfort (4 our of 10) and this lasts for about 2-3 hours. The neck pain is only about as uncomfortable as usual with a fever. Ibuprofen (2 - 200mg) takes the edge off the discomfort but after about an hour after taking it instead of sooner as normal. The headache is in the frontal and temporal lobe areas. No real sinus problems beyond the normal discomfort for this time of year. I have been highly stressed so I have blamed my problems on stress but now I'm getting worried. The discomfort is not completely debilitating but I have too much to do to just rest like I want to.