It sounds like you have done a wonderful job making Cooper feel safe and secure. My best friend had a dog that she "inherited" that had been in a house that was struck by lightening. He was scared of thunderstorms for the rest of his 11 years. He would crawl into the fireplace and the bathtub. She actually had to give him some benedryl before a storm was about to hit and it helped a lot.
I just know that Cooper's forever family will show up soon. I'll keep him (and your family) in my prayers that it is really soon