The musician in me would want you to double check how you position your wrists when typing. But if it's not a little carpel tunnel type of pain it could be trauma-related (sorry I teach, too, so get all motherly over arm joints). I wake up with headaches and don't know if it's related to bad dreams and/or tension in my sleep. I haven't sorted this out yet (I do have some violent nightmares). I have unexplained pain elsewhere but that was with me before I started SE in therapy and we're still working on slowly getting at that stuff.
My trauma responses and releasing involve more like shaking you described (usually good, but sometimes more like a "freeze" I need help separating). The shaking is sometimes really visible and uncomfortable and sometimes more like an inner trembling, like a low-pitched, slower vibration (that's usually a good thing for me). I also have breathing issues, and part of therapy involves bringing my breath back into a comfortable zone, whatever that involves (usually me feeling like I'm breathing through a tube, which would make perfect sense related to my trauma, but breathing changes are common with nervous system activation). Heat too...sudden shift to hot is not a good sign for me, soothing warmth all over is...so it seems more like good re-organizing is the more subtle stuff, but all kinds of feelings can potentially arise, and an SE therapist can help you help your body find a comfortable center point...and slowly our nervous systems reorganize.
I read Peter Levine's book and love that people like him are getting information out there on body-based therapies. I didn't really dare do the exercises much on my own. But it was sort of helpful for understanding this approach to therapy. In therapy it's very helpful because my therapist can help me find a resolution, especially for the uncomfortable body sensations. I hope SE is helpful for you. I'm really happy to find something other than talk therapy because there just aren't words for my stuff most of the time, but my body and my relationship to it has been a real mess.