Sort and wash beans, and place in a large Dutch oven. Cover with water to 2 inches above beans; cover and let stand 8 hours or overnight. Drain beans.
Combine beans and crushed red pepper in pan; add water. Bring to a boil; reduce heat, and simmer 1 1/4 hours or until beans are tender. Drain in a colander over a bowl. Reserve 1 cup cooking liquid; discard remaining cooking liquid. Return beans and reserved cooking liquid to pan. Stir in 1 teaspoon salt. Remove from heat; keep warm.
Preheat oven to 325°.
Heat oil in a large nonstick skillet over medium-high heat. Add onion and 3/4 teaspoon salt; cover and cook 15 minutes or until golden brown, stirring occasionally. Add bell pepper and garlic; cook 1 1/2 minutes or until bell pepper is crisp-tender, stirring frequently. Add tomato; cook 1 1/2 minutes, stirring frequently. Remove from heat. Stir in sugar, mint, paprika, and black pepper. Add onion mixture and 1/2 teaspoon salt to bean mixture, stirring well to combine. Cover and bake at 325° for 1 hour. Stir in vinegar.