Hello, my name is***** and I have over 20 years of experience as a veterinarian.
I am so sorry to hear about Ben. Many rescues adopted as an adult have some separation anxiety issues as they have already lost at least one family. You are correct that any sort of negative reinforcement after the fact is counterproductive. It only increases his anxiety and he does not connect the chewing destruction with your displeasure, he only feels more stressed because the person he loves is unhappy.
Most dogs would prefer to spend all their time with their very loved family to make sure that they don't disappear. This feeling intensifies for a dog that has already been rehomed at least once.
If he does well in a crate (not destructive) then I would use it while you are gone and at night. Many dogs can see a crate as a den. It's a secure place that they can be while the family is gone or when he needs to be alone. He needs to learn that if he goes in his crate you always come back and he is safe. Sometimes if they are out in the big house alone they just don't know what to do with themselves, get anxious and that can lead to trouble.
If you had a camera on most normal dogs while owners are gone you would see they spend most of their time sleeping. They are pack animals and if their pack members are gone then they rest up waiting for their "pack" to come home and play. So don't feel guilty about giving him a place he can feel secure in and rest in. In time as he realizes you always come home and come back for him, even if he cannot physically be with you then he may be able to be out in areas of the house but for now if his crate keeps him secure and out of trouble then let him use it.
If however he is tearing up his crate and is very anxious in it then that's not the way to go. Another option is to use a small bathroom at night where he cannot get into much trouble.
I understand initially he was fine in the kitchen. I suspect something happened (loud noise, wild animal outside) that startled him and being unable to get to you he panicked and became destructive. Dogs often use chewing and digging as stress relievers.
Ideally while you are working on training him he should only be left for short periods at a time. If you must leave him for longer periods you'll need a friend or dog sitter to come in and check on him, let him out to eliminate and make sure/reinforce that he's OK.
Work on leaving him for short periods of time (initially minutes) and always try and make coming and going boring, don't make a huge deal of it as that increases anxiety. Change your routine so that she cannot ramp up her anxiety about your leaving before you've even left. Pick up your car keys and walk around the house. Put on your coat and shoes and walk around the house.
Practice him going in and out of his crate or "safe spot" and staying there for a few minutes even when you are home. Give him indestructible play things (like a king ball stuffed with a treat he has to work to get out) that he only gets to do while he is in the crate, especially when you are gone. Find out what he really likes and reward him with that only when he is in the crate.
Leave a radio or TV on for company, initially both while you are home and away so that the noise level is the same, home or not.
Make sure that you ignore him for the first several minutes when you get home or let him out of the crate. Busy yourself with mail, or putting things away so that coming and going is never a big deal. Once you've been home for a bit then sit down and give him attention. Do not allow him to solicit attention however. Make sure you ignore him if he is asking for attention. If he stops then you can call him to you and give him attention. This way you are ignoring (NOT REINFORCING) needy behavior (attention seeking) and rewarding him with affection when he behaves independently and calmly.
If he is in the crate at night, in the morning too don't make a big deal greeting him, just let him out and then take him out to eliminate. You can then praise him and give him a treat for that.
Some of the OTC products for separation anxiety are safe and effective, but they must be used in conjunction with training. Medication alone almost always fails. Here are some links with training ideas that may help you:
As far as over the counter medications I do like DAP products (dog appeasement pheromones) which are synthetic analogs of a calming pheromone a bitch produces while nursing. These come in sprays, collars and diffusors. See this link for information about these products:
See this link for some examples:
I also like products made by Bach's Rescue Remedy: http://www.bachflower.com/Pets.htm
These products must be used in conjunction with training methods. If not they won't work alone. They simply calm him down enough so that he is able to learn. If he is terrified and extremely anxious then he won't learn to comfortably be alone.
If these aren't enough I would discuss medications, such as clonicalm or amitriptyline, with your veterinarian. He is fairly young and they likely won't need to be forever, just until he learns to trust that you are coming back and it is OK for him to be alone in his safe place.
We need to focus on building his confidence in general. A program that may help with that is called "nothing in life is free". This gives him confidence in your fairness and his ability to please you and where he fits in your home. Here is a link that better explains the program: http://k9deb.com/nilif.htm
A very relaxed, positive obedience course may help too. He learns how to please you, has positive interactions with you and will gain some self confidence.
By no means is this a quick fix, and he may have relapses, but we can help most dogs with separation anxiety with patience, training and medication to relieve anxiety.
Let me know if you have any further questions