Hi Saaby and welcome.
I am sure many will have great advice for you here.
I had MAGO treatment done for my TMJ and it worked wonders. I would still wear my appliance at nightime until i got my braces. There are several things they can do for your bite to help your TMJ. For me I didnt have any pain or stiffness until the 10th month and this came from clenching. I was fitted for a nighttime appliance WITH the braces and that got everything back in shape.
Talk to the Ortho about your concerns and ask them what they can do if you should run into pain or stiffness during your treatment. Good luck and keep us posted