Sorry that some of that information was repeating what you said. Rereading your question, I realize you likely follow sterile procedures and hygiene requirements at work. You're probably a clean person, being a CNA.
But again, if you've been sick this long and your doctor doesn't seem concerned, I'd check with another doctor.
I'm just going to throw it out there that one virus cannot "turn into" another. If you were ill and then contracted norovirus in addition to whatever was ailing you before, that was an additional illness, likely facilitated by your weakened immune system, not a replacement.
All I can suggest is to wash your hands thoroughly and often, and drink plenty of fluids (like water and juice, and also some green or herbal teas may help alleviate the body aches, and also boost your immune system) so you do not get hospitalized again. You said you work in a rehab clinic for surgery and stroke patients. I am assuming this clinic is located within a hospital or other care center. You could come in contact with any number of viruses or diseases in such a location, so proper hygiene is imperative for preventing further contractions. Additionally, eating well and getting plenty of sleep will help boost your immune system so you are not so prone to contracting this persistent bug.
Now, I am amazed you had flu-like symptoms for three months, and also that your doctor seemed baffled. I would think s/he would test you further to figure out what was wrong, and especially whether it was contagious since you work with recovering patients who could easily contract any illness you have. I would consult your doctor again, and don't take "I don't know" for an answer. You've been sick for almost four of the last six months it sounds like. That is a serious problem, and it sounds like your doctor does not realize this. Make an appointment, and be sure to explain the history of your ailments, and all your symptoms to him/her. There are other conditions which can cause flu-like symptoms, including diabetes and chronic constipation. Ask your doctor. Don't be turned away. You might even have an immune disorder if you're contracting illness upon illness for months at a time. Maybe s/he missed it because they were not looking for it in your blood work.