I'm like that too, both with hypersensitivity and hypervigilance so I get how difficult it can be. The hypervigilance drives my T a bit nuts at times, because I'd say something like, "Oh, you're shifting in your seat, so it must be time to stop," and she'd be like, "No, my hip was just bothering me." It's also caused issues in my marriage because I can sense when my H is angry or stressed, and then tend to assume it's about me. When often it's about work or something else. It's something we've worked on a bunch in marriage counseling. One way I deal with it is if I think, for example, that he's mad at me, I just ask him rather than assuming (though that often irritates him).

There's a whole series of books about The Highly Sensitive Person--one of them is a workbook. I haven't gotten that one yet, so I can't give a review, but that could be something to check out. And I agree on mindfulness and meditation--yoga has been helping me.