I know of a method to deal with holes, but I myself could not use it, even knowing full well it would be effective. It involves filling the hole with water, and giving the dog the impression the he will well be drowned in it (as in actually holding his head in it). This is from the same school of thought that says to take the chewed up shoe and tape it to the dogs mouth in such a way that the dog can still breathe, pant, but will be unable to remove the shoe. Leave for 6 hours or so. I have no doubt that the dog will not touch another shoe for the rest of his life. However I couldnt do any of that to my pooch (I guess I'm not russian enough?).
So my approach (thanks mainerdr!) has been to not let the dog form any bad habits. In other words, make damn sure that there are no shoes around for the dog to eat, ever. When he does get ahold of one scold him some, but keep in mind that its your fault for leaving the shoe there in the first place. For holes, make sure the dog is supervised at all times while outside. Once he grows up he'll loose the desire to dig if he never dug before.
The crate thing can be solved by serving his food in the crate, and letting him get to it volantarily. He'll likely not eat for a few days, but hunger will soon win him over. Also, never use the crate for punishment. Use the bathroom
Depending on the age, the peeing all over the place is pretty normal. They just dont have much control over that when they are young. Most dogs grow out of it just fine.
Side note: If you think dealing with holes is bad, try having a dog knock down a chunk of a cinderblock wall that surrounds the back yard.