I have suffered from migraine almost all my life and your son needs to see a doctor and try to find out what is triggering them. HAs he seen an optician lately, as well, because eye problems can cause headaches. Also try and look at his diet, exercise and sleep patterns.
Things that can help migraines include a magnesium supplement and an EPA supplement (fish/flax oil), regular exercise, eating small amounts regularly to help regulate blood sugar and things and having a set, predictable sleep pattern. Also making sure that he is well hydrated by drinking plenty of plain water, not tea/coffee or fizzy drinks because they are triggers for headaches. If his headaches are caused by stress, then I think that would need to be looked at as well, because the stress generated by missing school fuels the headaches and it becomes a viscious circle. I've been there and done that.
If he is at school, then it is the school's job to make reasonable adjustments to accomodate his needs and they should be looking for strategies that work. SOme things that might help are colour overlays for books, teachers making paper copies of the stuff that goes on the board for him to use, access to a quiet room or something similar, sitting nearer the front of the class. Perhaps some sort of peer support to help him keep up or access to school work via website/podcasts/powerpoints/recordings outside of traditional school hours. My DS1's school had things like chemistry lessons on line for kids who had missed them in class. Lots of subjects use technology nowadays that your son could bring home on disc or flash drive to use at home.
I think that the first priority, though, should be seeing someone who can help with his headaches. If you can begin to address the cause, then the rest should eventually resolve itself. It is possible that his headaches might be caused by his age and his hormones, though this is mostly a feamle problem. If that were the case, then he will probably out grow them.
If you want to think about HE, at 14 you wouldn't have to be his teacher. At that age, your son could be self guided and work when it suited him. My 17 year old has been HE for 6 years and has been almost totally self guided for 4 years, at least. He only comes to me for advice on specific things that he thinks I would know a lot about or for practical things like cooking/washing. Everything else he can find out for himself either in books or online. He has just subscribed, for example, to a site that will guide him through the higher maths syllabus because he was struggling with differentiation. DS2 is responsible for when and what he learns and it suits him very well. It might work for your son, as well.