That's a scary and frustrating position to be in. Having so many symptoms without a diagnosis can be worse that knowing it's a specific disease, even one known to be serious.
We're not doctors but since this is a forum site about bone marrow failure diseases perhaps we can help compare your son's symptoms to those of moderate aplastic anemia or even hypocellular MDS. Did his bone marrow biopsy show any problems in his chromosomes?
Does anything in his/your family history provide a clue?
His exhaustion and headaches fit with the low red cell count often seen with aplastic anemia. A low white count from AA could leave him prone to infections and some of those symptoms could result from infections. Could you be more specific about what his blood counts have been like?
Even though those symptoms match what we often hear in these forums, the variety of other symptoms (skin problems, photosensitivity, swollen eye lids, inflammation, mostly suppressed appetite, pain in his knees) doesn't match the profile of a typical pediatric AA patient. I can see why you and the doctors are having trouble solving this puzzle.
Your son may have a combination of disorders, and when any one of them is rare the combination is even more rare and harder to diagnose and treat.