Hi, Patty!
The pain in your eyes *is* common with Graves’ Ophthalmopathy. I
experienced the eye aches and headaches also, especially in the
morning. My eyes weren’t closing completely at night, and they were
drying out. They were red, watery, and itchy. The only thing that
helped ease the discomfort was using an eye lubricant and literally
taping my eyes shut with 3M’s sensitive first aid tape at night.
I also used Allergan’s Celluvisc eye drops during the day for those
extra-dry days. With time your eyes will get better, it just takes
some patience on your part. (I know, it’s frustrated!!)
Patty, if you haven’t already seen one, you need to see an
ophthalmologist that knows about Graves’. Your eyes’ progress
need to be monitored closely, and s/he may have other suggestions
for your individual case.
Your endo is probably correct in saying that part of your symptoms
may be due to stress. Even after all these years, my eyes still get
irritated when my stress level is elevated. This too shall pass.
Don’t give up, warrior! 
Wishing you health and happiness, Debby