It sounds like you have recovered from the surgical proceedures after the Hematoma. You did not say how long ago it originally happened or what the originally caused the hematoma. Was it due to traumatic incident?
The nagging, spreading pain that goes down your neck and sometimes into your back is probably muscular in orgin and may respond well to treatment with Neuromuscular dentistry but a lot more information is needed. You stated that the pain goes down your neck but even though it feels like that, they may actually be pains comig up from the back to the neck. Neck and back pain are closely related to jaw pain due to posture. Your exam should include a thorough muscle palpation exam to evaluate trigger points and sore muscles.
The suden shooting headaches are probably neurologic in nature and I hope you have discussed them with your neurologist. That pain may have a specific trigger. It may or may not be affected by neuromuscular orthotic treatment. When you receive an orthotic it can help problems that are due to nervous overload.