Sue, Have you had a sleep study done? I imagine that would be the best way to figure out why you are having trouble breathing on your back. I never sleep on my back due to my MG.
The thymus is really small and if you had a thymoma, unless it was huge, it would probably not cause a problem with breathing while on your back. In MG, it's the chest wall muscles that get weak that cause an inability to breathe well. In autonomic disorders, it can be many things that cause an inability to breathe.
Have they thought about sending you for autonomic testing, due to the inability to sweat, etc.? Have you been evaluated by endocrinology?
I don't know who told you that you have a "hump" in those bones but I think they need to be a bit more scientific and specific!

Is it a bone spur? Some genetic thing? Can you pulmonologist answer those questions?!!!
I hope you get it all figured out.
Annie