Possibly. You may have no alternative but a combination of orthodontic treatment and jaw surgery to find comfortable jaw joint relationship, align teeth to the jaws, then reposition the teeth/jaws surgically while maintaining the comfortable joint relationships. Make sure you're seeing an orthodontic specialist and an oral surgical specialist.
Yes. It is important to have a well qualified and trained individual evaluate your tmj/jaw anatomy, condylar position and relationship of the upper and lower teeth. Perhaps this has already been done? If not, i would do this before proceeding.
POSSIBLE . Would not be unheard of.
Jaw position relates. The position of your jaw determines the position of the jaw joint. The position of the jaw joint determines how the stresses inside the joint affect the joint structures. An abnormal jaw position can therefore affect the joint. You need to find a stable joint relationship first and then treat to that association. Tmj orthodontics is one way to manage this problem.
Maybe. If you had no TMJ symptoms before orthodontic treatment and TMJ symptoms started during treatment, it is possible. Depends on other variables. See a TMJ expert to sort things out.
Possibly. Your treatment puts your bite in a state of constant change. As the teeth are moving, your biting surfaces are changing. It is likely that you have no "home base" for your teeth to settle into place and allow your jaw to rest. Your jaw muscles are potentially stressed all the time. Your muscles and joints need to rest, and are seeking a place, anatomically, to rest. Ask orthodontist about adj. .