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2 months ago life fell apart--Dr's have no answer


I am writing in a hope that someone can help.  I am looking for a place to start.  I have begun conducting research on my own, becuase two months ago, my boyfriend got sick.  He had what we thought was a kidney infection, however, at the time we did not have medical insurance (changed jobs) and he had to wait almost two months before we could see a primary care doctor (we went to a clinic, but no help).  

We have considered everything from Lyme disease to Vasectomy complications, but there appears to be more similarity with autoimmune disorders.  

MAJOR FATIGUE, he can barely get out of bed, feels tired no matter how much sleep
foot pain, swelling of left knee, leg cramps and muscle twitches, cant sleep becase he is so uncomfortable, complete loss of sex drive, and naturally depression becuase he does not know what is happening, and so many more, it seems like everything is falling apart.

The change in him has been dramatic and sudden.  
We were finally given a referral for a rheumatoid specialist (its a start=) and, I am hoping someone out there can help with questions we need to ask, what types of tests for which problems, etc.

Any help would be appreciated.
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