Wow, kudos to you for working with your boy for all these years! I'm sure your patience has been tested so much, but don't give up! Many great suggestions have already been said, and I'm sure I'm repeating some, but I'll throw out my ideas too.
First rule out any medical issues. Like others mentioned, thyroid can cause behavioral issues. You'll need to run a full panel, not the in-house tests. They'll need to be sent to places like MSU or Antech. Also check with your vet and a behaviorist about anti-anxiety meds. This sounds a lot like some severe separation anxiety. A good behaviorist would be a nice consult anyways.
As far as some changes you can make around the house, I would try the DAP products that release a calming type chemical. This may not help as much, and you may need a stronger prescription type med like others mentioned, but it's at least worth a try. Also do you have room in your kitchen for a 4x4 X-pen? He might not have as much issues if he's got some room to move around, especially if part of his behavioral problem is crate phobia. Or at least he'll be less likely to mash his mess all over the floor with extra room. You'll need to get a top for the X-pen as I'm sure he'll figure how to get out easily, but once you put a top on it they're fairly sturdy. You can buy some cheap linoleum roll at places like Hope Depot that you can put down on top of your kitchen floor or any other surface where you need to put his crate/pen. That will keep him from destroying your "real" flooring at least. You can put a crate or half a crate in a pen as a den or bed, and you could even try putting in a litter box of sorts to see if he'd bother using it, since he tends to go to the bathroom. You can fill a big cat litterbox with shredded newspaper or wood pellets for a potty area.
Also try to put some interesting and time consuming treats in there to keep him busy. Frozen marrow bones, and kongs filled with stuff (dog biscuits, cream cheese, peanut butter, etc.) and you can freeze them too. Whatever you can find that will be safe for him to chew on and tasty.
Sometimes adding another dog can make all the difference in the world. With a buddy, he might be so much happier. HOWEVER, it sounds like you have less and less time these days so it might not be the wisest idea. If you do add another dog sometimes it's easier than one, but you have to be prepared for it to be even more work!
And of course exercise exercise exercise! I can't stress that enough. The more you can get Buddi tired, the better he will be. I know it's hard to find time with a busy work schedule, but try to sqeeze time in in the morning and night to walk him. Even better (and easier for you) would be biking him. It will tire him out quicker than just a stroll down the block. He might need to run for a few miles to work out some of that stress. And you could even look into something like weight pulling where he's going on walks with you but dragging a little weight as well which will wear him out. Also mental stimulation will help wear him out. Try to find an obedience or rally class to take him to between your busy schedule. Learn some training exercises you can do at home and work with him when you have a few minutes of downtime in the house. Also make him work for everything he gets. Like make him sit and do a few tricks before giving him his meals, etc. Not sure if you or your husband have any free time on the weekends, but you could look into trying some lure coursing with him if there's any in your area occasionally. That will certainly tucker him out! But unfortunately it's usually not a "regular" activity in most areas.
Everyone already had some great suggestions for re-crate training and making that a more positive experience, so I won't touch on that. Make sure though when you come home, that you don't make a fuss over him. Ignore him for a few minutes and then calmly greet him. I guess that's all I can think of for now.
Keep us posted, and we're all pulling for you and Buddi!
