Place salt cod in a large glass or plastic mixing bowl with enough cold water to cover, and let soak for 24 hours in the refrigerator, changing the water two or three times. Put beans in another bowl, cover them with cold water, and let soak for 24 hours in the refrigerator.
Drain beans. Transfer them to a medium saucepan, and add fresh cold water to cover. Bring to a simmer and cook gently (do not boil) until beans are tender, about 40 minutes. Add salt after 20 minutes. Strain beans and reserve some of the cooking liquid.
Drain salt cod and trim off any brown flesh. Place cod in a medium saucepan and add milk, peppercorns, and bay leaves. Simmer over medium-low heat until fish is soft and flakes easily, about 20 minutes. Remove from heat, strain fish from the pan, and place in a bowl. Use a fork to flake cod into bite-size pieces. Discard milk and seasonings.
Melt butter in a large saucepan over medium heat. Add garlic, carrot, leeks, and thyme, and cook for 3 minutes, stirring occasionally. Add clams and wine, stir, and cover. Cook just until clams open, about 7 to 10 minutes. (Discard any clams that do not open.)
Add cod, beans, lemon zest, and parsley and stir; add some of the bean-cooking liquid if the stew seems too thick. Ladle stew into small bowls, drizzle with olive oil, and serve.