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Haopee has offered some excellent suggestions. I thought I'd offer something from my own experience as it might be helpful to you. You might search for some of my posts. I have a Jack Russell. She was treated very well as I got her at 8 weeks old. But, right before her first birthday, two events happened that threw her into a tailspin. My Dad was hospitalized and died (he lived with us) and a neighbor who visited with him everyday moved.
I had to move after that. It was an unsettling time. Misha had a bit of a nervous breakdown. Once I was settled in, she had several problems. One was peeing in the house even though she was housebroken (Jack Russell's are notorious for being slow at housebreaking, by the way), she ate carpet, and she became violent when anyone attempted to pick her up.
I won't go into all the details of what I did. But, I went back to dog training 101. I acted as if she had learned nothing and started over. I think, though your dog has different issues, this is probably what you should do. Don't baby him too much because he has been abused. This may make things worse. Show affection but don't let him get away with things because of his past. He may need some gentle handling in certain situations. But, give him dog training so that he learns to trust you. It was the one problem I had with Misha after our emotional trauma. Earning back her trust was the hardest to deal with. But, she is three years old now, and despite a couple of quirks, she had turned into a fine dog.
A forewarning, Jack Russell's like to be in charge. You'll have to work on letting him know you are the boss. I did this by teaching Misha to sit for food and to wait for me to enter the door first. It's the little things that will help your pup out.
One thing in your favor is that Jack Russell's love to learn. They love to please and they love to do tricks. You can set up a really nice trick and reward system that should help your dog trust people. Good luck and keep us posted on how it is going!
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