Here is a good site to look at the far-reaching affects hypothyroidism may have. It also lists the corneal ulcers as a potential symptom of canine hypothyroidism!
http://www.canismajor.com/dog/thyroid.html Here is another
http://www.canine-epilepsy-guardian-...muneSystem.htm it also lists the corneal ulcerations as a symptom along with several other eye problems.
As far as a specialist -- I would look toward the university veterinary schools and see if they have an endocrinologist specialist.
Good luck!