Wha to do, what to do.....sick hubby.....

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Maybe someone out here can give me some guidance. My husband has been sick on and off for about 2 months. He will out of the blue spike a fever (100-102), get body aches, sometimes shivers, moderate to severe headache. Normally motrin will bring the fever down, he just goes to sleep and when he wakes up he is fine. His primary Dr says that its chronic sinus' and sent him for a head CT last week and told him to take Amoxicillin after getting the head CT. If the fever came back to motrin. Last night he had another fever (day 5 for the Amoxicillin), it hit 101 and we could not get it down. We called the Doctor on duty and got the okay to go to the ER. When we arrived my husband was really sick, of course after waiting 5 hours by the time the Dr saw him my husband was fine. The good thing that came out of the ER is that we found out that his head CT was clean (so no chronic sinus anything er the ER Dr). Of course, that was not what we expected to hear. Unfortunately since the blood work was done at the military clinic, the Dr unfortunately could not see the results. The only major changes in his health history in the last year is he had shoulder surgery October 2009, he got the 3rd Hep A/B shot this spring, and in September he got the flumist (which he got last year and did get sick form, same this year). A TB test (negative results) was done on 11/17 when his blood was drawn. The flumist shot is around the time that these fevers started, but the ER Dr ruled that out since the head CT scan was clear and his brain looked "good". The only other thing - and we did mention this - is that we had surface mold in out bathroom a few months ago, but it was treated and has not come back (viably at least). No one in the house has the same symptoms. Any idea of what he could have? I'm trying to research this myself, but unfortunately these symptoms are symptoms of just about everything. I'm concerned that he has some weird auto-immune disease or - even worse - something that he picked up form traveling outside the US years ago that is just now showing up.