Hi intentional-breather.
Headaches are way too common in my life as well! Regular painkillers work for me but I should be eating them 24/7 if I'd want to be totally headache free!
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I have figured out that there're certain reasons that cause my headache:
1. an alter lets me know if I've understood her/him wrong
2. an alter lets me know if I've written wrong info about her/him (I have a list of my alters and their features written down)
3. an alter is trying to get my attention
4. headache comes allways after full switch - doesn't happen too often though
5. an alter is giving me body memory (I remember having constant headache during my teenage years)
6. overlapping chatter of 10 alters or so at the same time causes headache
7. being just simply too stressed out
8. an alter that is trying to get him/herself heard but lacks the strength
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Here's just something that I know right now. I'll try to relax as often as I can, it seems to help with my headache a bit.

At least one of my alter just said so! Maybe you could ask your alters? They seem to know quite a lot about my headaches - maybe yours would know too?
I hope you get your headaches to stop or at least get them less sharp! :/ It's a nasty thing to have!
EDIT. Oh, almost forgot to add one thing!
9. an alter is suffering of headache (I have many alters that have had that problem)
I've also noticed that when I realize what headache is mine and what is my alter's, the amount of headache decreases with all of us.