In a large bowl add beans and enough water to cover by 3 inches. Soak at room temperature at least 8 hours or overnight. Drain.
In a 6 to 8-quart Dutch oven cover beans with fresh water; bring to boiling. Drain. Rinse beans once.
Wrap garlic, thyme, and peppercorns in cheesecloth. Tie with 100-percent-cotton kitchen string; set aside. In the Dutch oven heat the oil over medium heat. Cook onions, cut-side down, 5 minutes or until golden. Add chicken broth, cheesecloth packet, and the rinsed beans. Bring to boiling; reduce heat. Simmer until beans are fully tender but still hold shape, stirring occasionally, about 1 hour. Add broth as needed to cover beans. Drain, reserving 1 1/2 cups cooking liquid. Discard cheesecloth packet and onions. (The beans can be prepared to this point up to two days in advance.)
In a Dutch oven cook drained beans and 1/2 cup reserved cooking liquid over medium heat. Add butter, one cube at a time. Add 1/2 to 1 cup more cooking liquid until consistency. Cook and stir until butter is incorporated. Season with salt and pepper.
In a small bowl combine Parmesan, parsley, lemon peel, and crushed red pepper; sprinkle on beans. Top with Seasoned Bread Crumbs.
Seasoned Bread Crumbs
Preheat oven to 425 degrees F. In a medium bowl toss bread cubes with oil to coat. Spread on a 15x10x1-inch baking pan. Bake, uncovered, 8 to 10 minutes or until golden brown. In a food processor combine toasted bread cubes, lemon peel, thyme, and garlic. Cover and process until coarse crumbs form. Makes 1 cup