I'm about to explore this possibility with my doctors. I just received a referral to an infectious disease specialist from my primary care physician. I presented research suggesting many correlations between rather common and often dormamt infectious diseases and TMJ symptoms. Some examples of such diseases are Lyme and Clamydia, among many others. There is no experimental smoking gun, but many of the charateristics of TMJ symptoms seem consistent with an infectious disease etiology. Infectious agents include viruses, bacteria, and fungi.
Perhaps severe bruxing is often a result of the derangement of the trigeminal nucleus in the brain. Perhaps peripheral stimuli, such as uneven bites or certain traumas trigger a neural mechanism that would lead to mild bruxing in most, simply to even out the bite and perhaps adjust breathing patterns during sleep, were it not for the influence of an infectious agent. Perhaps severe bruxing is the result of an adaptive neural program kicked into overdrive.
We know that severe bruxing can have a central (neurological) root, as is evidenced by bruxing caused by certain psychotropic drugs. It's hard to see what adaptive purpose severe bruxing can serve and it's interesting to note that severe bruxers often continue bruxing even after having all teeth removed.
It's little more than a shot in the dark, but one certainly worth taking, especially as this cause could underlie a significant portion of TMJ manifestations.