Hi there,
I also got really sick with a virus, a little over a year ago, and I had a bad cough along with it. After that I began to have pain in my hands and knees, and now 16 months later, and three negative RA tests, my only answer is unspecified inflammation. I know you mentioned in your post about your hips, the pain is now in my hips as well, and the pain just gets excruciating. 
In the beginning I went through all of the NSAIDS, but they didn't work and were hard on the tummy! I tried plaquenil but after 3 months my doctor said it should have been working, stopped it and put me on the sulfa. I tried it for a week last month and ate nothing but crackers and diet 7-up, the nausea was something else. So I went a month without any medications, and last Friday I went in for my checkup and I am back on my plaquenil, and a Medrol dose pak.
All of my testing has been normal, everytime. However, I have joint swelling in my fingers, knees, and sometimes in my elbows even. But the worst pain is my hips, when I have a flare, such as now, I think I am going to lose my mind.
It sounds like you may have an infection somewhere, I sometimes feel warm to the touch, but when I take my temp, it is actually low, sometimes as low as 97.0.
My doctor actually thought mine was viral in nature at first, but after a few months, decided against it. I was tested for the same virus because I was teaching preschool at the time.