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Couldn't it still be the brain sending dysfunctional signals to the nerves?
I for one have a ton of sensations around my head. The worst is this constant pulling/pressure kind of sensation behind my eyes. My jaw is tense, neck is tense, shoulders are tense.. I get tickling, tingling, burning sensations around my eyes and temples that come and go. Today I had a pretty severe headache but those aren't every day. My neck is also twitching a little. If I get angry, upset, nervous, excited my neck starts shaking really badly and trying to turn my head is very stuttery. My hands will start shaking too, same as my voice.
Typically its much more the case that these nerves supply sensory input to the brain rather than the brain supplies input to these nerves but there could be some modulation of these nerves by the brain. There could also be some dysfunction in the brain in that would take some time to resolve after the cranial nerves calm down.
The main brain region concerned here is the somatosensory cortex, but there are other brain regions that process the information from cranial nerves before sending it off to the somatosensory cortex - the thalamus processes the information beforehand and then communicates with a large system called the reticular activating system (RAS) that is intimately involved in many processes, including sleep and sleep related paralysis.
The RAS and somatosensory cortex are both in a position to cause a lot of these symptoms, so I suspect the cranial nerves are causing dysfunction of both the RAS and somatosensory cortex at once. The RAS is really hooked in to our fight-or-flight systems - I suspect that excess input from the cranial nerves -> thalamus -> RAS can cause a lot of the sympathetic stress response symptoms.
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If I try to hold eye contact and talk I get this feeling of confusion. It is difficult to describe but it's like I can't process all of the information"
The somatosensory cortex actually has a lot to do with social interaction and empathy and processing such complex social information that we receive through our senses, I think somatosensory cortex dysfunction can account for these reports of social abnormalities and some somatosensory cortex dysfunction has been spotted in chronic MDMA abusers in a neuroimaging study.
I don't know exactly whats going on with the cranial nerves, but it could be that there is some inflammation and aberrant activity that needs time to calm down. Fixing posture would be important if you have hunched shoulders/spine and forward head posture.
There are meds like Lamotrigine that see use in treating cranial nerve disorders (in addition to epilepsy, migraine and mood disorders), so I've always been curious to see how it would affect the cranial nerve related LTCs.
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I still sometimes get these seizure/stroke type episodes (or days) when I just feel like absolute death and so confused and out of it I'll just sit and breathe. "
Watch out for respiratory alkalosis with hyperventilating - hyperventilating can result in quite a lot of symptoms, especially pins and needles in the face and extremities. Eventually the muscles will start to spasm uncontrollably. Long story short, there is such a thing as too much oxygen and not enough carbon dioxide.
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If I get angry, upset, nervous, excited my neck starts shaking really badly and trying to turn my head is very stuttery."
Heh, yeah I used to get this pretty badly, the back of my neck would start contracting, I probably looked pretty spastic lol. But needless to say I haven't had this happen in forever.
Try to slow your breathing down and try learning some mindfulness/vipassana meditation. Breathing too much is no good, and it will just make us feel more out of breath in the end.