tree and ceee,
I understand more of your situation now. It sounds like you have medical experts on your side, which presumably means they will eventually reach a proper diagnosis. Without that there's little way to know what the long term holds for your son. That's a huge burden, as it would be to any parents with a sick child.
In the meantime, pain should not be ignored in any patient and it's terrible that they aren't paying proper attention to it. This happens far too often, which I think is because doctors sometimes concentrate on the illness more than the patient.
I think it means you will have to be a squeakier wheel and be more demanding (while staying polite) as you advocate for your son. You might also look for a "patient advocate" or "ombudsman" or someone equivalent at the hospital and enlist their aid in working within the system to get more answers and help for your son. Maybe they have pain specialists who can become part of the team.
Since relief from the illness doesn't seem to be around the corner, I think you should ask about pain medications that would be appropriate. If they don't seem inclined to use them to give him relief right now, ask why not. It doesn't necessarily have to be prescription medicine, but you should have an OK before using over-the-counter pain medications regularly. Living in pain is likely to sap anyone's spirit and make them feel more helpless than they are. And when he hurts, I'm sure it hurts you too. Even having some medicine to "take as needed for pain" would give you and him more control.
Are your son's pains worse when his red blood count is lower, and better when higher? If so, he may need more frequent transfusions despite the risks such as iron buildup. Every doctor seems to have a different opinion about when to do transfusions based on HGB or other factors, and I'm sure you could influence that decision.