Hello~I am sorry you are having these miserable symptoms. It sounds to me like you may have Chronic Fatigue Syndrome, Fibromyalgia or Epstein Barr virus. Ask your doctor for some blood work to rule out the EBV. Fibro can certainly cause pain all over and it does, indeed come and go. The headache could be due to low blood pressure when standing up too quickly called Orthostatic Hypotension.
I suggest adding a high potency B complex to your diet and cutting out all sugars, these will help keep your immune system stronger, but, again, as I said, it really sounds like one of the three diseases I mentioned above. I would certainly ask your doctor about them.
You might have glandular fever aka infectious mononucleosis (mono). There are plenty of forums on discussions about mono talking about symptoms including flu like symptoms and muscle pain, labs not showing up positive until months later, symptoms going away and coming back. Not a very nice virus.
Do you have any fatigue at all? Severe compression of either the Renal Vein (Nutcracker Syndrome) or the Iliac Vein (May-Thurner Syndrome) can cause the problems you’re having. Check out some of these groups on Facebook. A Vascular Surgeon might be a good doctor to go see.