Everytime I have a long flight I'm hungover the next day. Oddly, it almost seems worse when I fly first class.
Headache can easily be dehydration. You lose a cup an hour of fluid in flight. Drink lots of water before during and after.
For the rest, are you in good cardiovascular shape? The cabin pressurizes to 10k or so feet. It could be that causing you problems, but a doctor might be able to tell you if that is caused by a bigger problem.