Bless you for rescuing a puppy mill survivor!
For our toy poodle's separation anxiety, I used one of those Comfort Zone plug-ins and it did help alot. It's available at pet stores, but I got ours from the Drs. Foster Smith website, because it was cheaper. To save money on refills/make it last longer, I would only plug it in near his "cubby" (what we call his carrier/crate) when we had to leave the house. I also left a white noise machine on and turned the lights down low. What eventually helped Squirt the most though, was adopting him a buddy. After we rescued our yorkie-poo Rascal (from a local shelter), Squirt's separation issues lessened dramatically. Bless your little Joey's heart. After living in the puppy mill setting, it's no wonder he has separation anxiety.
Again, kudos to you for rescuing him. This world needs more people like you, willing to adopt an older dog with a difficult past.