Sometimes allergies can cause dogs to have bad odors on their feet, in their mouth, their skin/fur, and in their ears. This isn't normal! You may want to see if there's a holistic vet close to your area who has experience with allergies and nutrition. You may also just want to go to another regular vet for a second opinion. There are any number of possible reasons for a bad odor, including skin conditions or another internal health problem.
Has he had his anal gland checked? While it's more common for small/toy breeds to have problems there, it's not unheard of for other dogs to have anal gland infections or to need to have them expressed occasionally. They make the dog smell TERRIBLE if they are full or infected, and no amount of bathing makes the smell go away because the problem is internal. If that's the problem, a change in his diet may help prevent it from happening again.
It may also be something simpler, like walking in or eating his "business" after he goes potty. If he goes out unsupervised, you may want to go out with him to see.
If he's not a picky eater, you may try giving him raw carrot pieces for his breath. My dogs love them and it makes their breath smell a lot better. They also sell minty dog treats that doa great job. At two, he shouldn't have build up that would cause bad breath.
Is this your first Schnauzer? I'm not very familiar with the breed, but is it possible that this is a breed characteristic? If this is your first one, you may want to contact a good breeder to see what health problems the breed is prone to.
In short, I'd try another vet who will check things besides his stinky feet. There are too many possible causes for bad odor, and none of them are untreatable.
Good luck, and give your fur kid a scratch for me.
T.