I wish I knew. We have a very similar problem with DD (13) who has had the same sort of thing since, I'm afraid to say, the beginning of September.
Can you pinpoint when your DS's condition began? For DD she had a violent allergic reaction to something or other (no idea what - have drawn a blank)and came out in hives. Emergency overnight trip to Out of Hours docs and was given intravenous anti-histamine and steroids. She has been ill pretty much since then. She has some absolutely normal days where there are no symptoms at all, and then, from nowhere, she'll develop a bad headache. Early mornings and bedtime are the worst times, although she has missed some social activities during the day too.
She loves school, but her attendance has dropped to 76% this term! We have taken to dropping her in later on bad days, once she has perked up. She's technically old enough for tablet pain relief, which I thought might be more effective than Calpol/Nurofen, but she's always struggled with tablets and gags on them. Currently we're insisting that she drinks loads of water, which seems to help a bit.
What does your GP say? DD has been referred to a consultant paediatrician and seen him twice, but no real help, to be honest. He's suggested ways of managing her routine and says that we can't do any more tests (bloods/urine etc all been normal since Day 1) until 6 months, whereby it'll be clearer to see if she has ME. In the meantime, we have to persevere and apparently it's "not uncommon."
He's offered ideas that are used with ME sufferers, such as not overdoing things when she's well, yet not collapsing into it when she's suffering, sort of following the middle path.
We are now wanting to look at alternative remedies - massage/food intolerance/whatever, so I'm very interested to watch this thread. Don't really know where to start. We're all fed up to the back teeth with it, as I expect you are too. How much is it impacting on your DS's life?