Hi
So sorry to read of your problems
As you have posted in the hepatitis community do you have hepatitis.
You may want to try your question in the respiriotry disease community
http://www.medhelp.org/forums/Respiratory-Disorders/show/61
I looked briefly at information about Hashimoto's did see anything about breathing but you probably know that already
http://www.mayoclinic.org/diseases-conditions/hashimotos-disease/basics/symptoms/con-20030293
But really the only way you can get help beyond advice is from a medical professional. Are you being seen by a respiriotry specialist?
Good luck to you
Lynn