It's really refreshing to hear you're doing so much for this dog. So many people buy a dog and don't do what's best for the dog. I am happy to hear he has made such progress!
I didn't read this entire thread so I apologize if I repeat what others have said. Aa far as the separation anxiety. Are you following what Tia said to do? All my guys had separation anxiety, but I was able to cure it. As adults, they are very content being alone. Make sure you are putting him in the crate when your home too. Walk out of the room for 5 minutes and come back when he is quiet. If he is crying, shout quiet from where you are in the house. The second he is quiet, walk in the room but don't look or talk to him. He might be whining, but ignore him until he is quiet. Then turn to him and say, good boy! You should do this several times a day when you are home. If he doesn't quiet when you shout, you can make a loud nose along with saying, quiet. I used bongo drums
My guys were easier because I got them as pups. Bella was the oldest at 7 months old. I would say they stopped the barking after a long weekend of doing this many times throughout that weekend. Now when I leave, I always give them a treat and tell them I am going to work. I think they actually look forward to me leaving. I hope this helps! Good luck.