I had a thunderclap headache and I'm wondering if I can still join

Not without a waiver, a thunderclap headache is indicative of something that can possibly be very serious and very life threatening. While the military seems to provide waivers for pretty much anything at MEPS, for something as serious as that you may be able to swing it if you're going for a crucially undermanned job that is hard to qualify for. Your chances are not very good if you aren't trying to go for an extremely specialized and rare position.