Instead of braces, I had retainers when I was growing up. I had a variety of different ones that, among other things, spread the roof of my mouth and realigned my bite.
Later, I had a lot of tmd issues. The dentist said that a lot of times orthodontia can actually CAUSE or exacerbate these issues. I got a different splint/retainer which allowed my jaw to return to a more natural position, after which he adjusted my bite slightly. Since then I have had very little trouble with my jaw (I do still wear the splint at night only to prevent grinding my teeth).
I would suggest that you find out if your dentist is Pankey Institute certified and, if not, maybe get a second opinion from one who is. You can look this up here:
http://www.pankeydentist.org/