What can cause eye shrinkage, pain? One eye bigger and higher that the other. (photos)

Thank you for the pic.  You have some lid retraction on one side that leads to the eyes appearing different.  You have done the right thing by seeing your eye doc.  I would go further and seen an oculoplastics doc.  Sometimes the thryroid tests can appear negative, but you still have a thyroid problem.  Make sure the doc send for antibodies to the thryoid.  The ache you are having can be caused by dryness on the surface of your eye or an incorrect eye glass/ contact lens prescription.  There are also diseases within the eye and in the orbit that can lead to this sensation....  Best of luck.
Dr Z

You have what appears to be lower lid lag and some proptosis, but an examination is needed to tell for sure and evaluate for possible solutions.  

Thank you for sharing your case and photo.  I'm sorry to hear that you are having such difficulties with your eyes. Because it is difficult to make any recommendations based on your photo, I would recommend a second opinion with a board certified oculoplastic surgeon to discuss your concerns and be examined in the office.  You may want to bring a copy of your blood tests and your scan to the visit.  Good luck!