What you say makes a lot of sense. Misalignments of the facial and cranial structures can affect the teeth, and vice versa.
Cranial osteopaths and other practitioners can correct these misalignments. The St. John Neuromuscular Therapy Institute in Florida developed some new techniques to stabilize the facial, cranial and cervical structures and began training practitioners last year.
I had the good fortune to be treated by one of the first people trained in these methods and it immediately realigned my tmj such that it stopped the jumping/popping/jerking when opening and closing. I can open my jaw normally now and without the crunching/crackling/grinding noises.
A possible cause of the shooting pains in your eye could be trigger points in the muscles of the head or neck.
What's the report from your oral surgeon?
------------------
~p
| 
Alignment...shooting pain... 
Linear Mode
