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Huckleberry,
It is interesting that you would ask this question today, as I just read an interesting theory yesterday that offers an explanation for the phenomenon of waking up with pain. I have been diagnosed in the past with Fibromyalgia/Chronic Fatigue Syndrome which I now understand to be TMS. One of the classic symptoms of fibromyalgia is waking up with pain and fatigue. In trying to understand this in terms of the TMS paradigm, I've been reading a book called 'The Trauma Spectrum' by Robert Scaer, M.D. (2005). And there I found a plausible explanation. I'll quote his words as it's rather complex and I don't want to get it wrong by rewording it. Dr. Scaer (who is a neurologist and trauma researcher) states:

"Interestingly, the phenomenon of awakening with pain in fibromyalgia and other trauma-related skeletal pain syndromes is linked to, I believe, a symptom of muscular bracing combined with abnormal vasomotor tone during the dream--or rapid-eye-movement (REM)--cycle of sleep. As I have noted, one of the roles of dreams is to integrate the day's stressful or threatening experiences with past procedural memories of threat and trauma in order to replenish and expand the survival brain's storehouse of remembered survival skills. In the victim of complex trauma, this storehouse is overflowing with memories of danger. Accessing these memories at the onset of dreaming sets off muscle bracing in patterns of learned attempts at failed self-defense from old traumatic experiences. The muscle bracing reenacts what the body did during the traumatic event. It also sets off activation of autonomic cycling that causes abnormal patterns of constriction and dilatation of blood vessels, primarily in the regions of the body that were involved in these old traumatic experiences. Constriction of blood vessels in muscles that are contracting causes severe pain, as in a heart attack. This leads to immediate awakening with pain, often in the core of the body--the head, neck, or back--which must be braced before any other self-protective behavior can begin. Therefore, the symptom of awakening with pain is, at least in part, related to arousal, or the sympathetic limb of the exaggerated autonomic cycling in trauma."

I apologize for the length of the quote, but it all seems relevant to the explanation. This makes sense to me and fits with Sarno's theory of TMS. I'm now researching what to do about it, and so am reading Peter Levine, PhD and his Somatic Experiencing process.

I hope this helps with your understanding of your pain on awakening.

Ellen