I'd try a different type of crate and see if that helps, and I'd definitely see about changing/increasing meds. Just like people, different dogs need different things. When you leave him out, does he have free roam or is he contained in a room? I had a foster that could not be crated and we ended up leaving him in our guest room and it worked really well. I think his anxiety was different though, crate anxiety, not separation anxiety.
Poor guy. He must be a wreck when you are gone. I hope that playing around with his meds works for him.
I don't know if this is even valid or safe advice, so take it for whatever it's worth to you. But, what about a muzzle and booties? I am not sure it would be safe to leave him unattended with a muzzle on. It also could add to his stress level. I don't know just an idea.