On Tuesday I had my first appointment with Dr. Kaplan, a TMJ specialist. She was very thorough in my examination, taking multiple measurements, listening to my jaw with a stethoscope, asking many questions about my history of trauma/injuries, and taking a tomogram. She also took an impression of my bite so that she could examine it and also use it if I needed splint therapy.
Well, I got a call from her late last night and she found some significant distortion in my left TMJ. She was surprised that I wasn't in more pain. This is something that has been going on for a while, and the orthodontic work made it flare up.
I am happy that I now know what the problem is. Her recommendation is splint therapy on my bottom arch. Planning to run this by my dentist before I go forward with it, but I don't think there are any other alternatives out there.