To prepare soup, sort and wash beans; place in a large Dutch oven. Cover with water to 2 inches above beans; bring to a boil, and cook 2 minutes. Remove from heat; cover and let stand 1 hour. Drain.
Combine boiling water and chipotle chile in a bowl; let stand 15 minutes or until soft. Drain, seed, and chop.
Heat oil in a large Dutch oven over medium-high heat. Add onion; sauté 2 minutes or until tender. Add garlic; sauté 1 minute. Add beans, chipotle chile, 2 cups water, oregano, cumin, and broth; bring to a boil. Cover, reduce heat, and simmer 3 hours or until beans are soft. Place 1 cup of soup in a blender; process until smooth. Return to pan. Stir in pepper and tomatoes; cook until thoroughly heated.
Preheat oven to 350°.
To prepare toppings, place tortilla strips in a single layer on a baking sheet. Lightly coat tortilla strips with cooking spray. Bake at 350° for 12 minutes or until toasted.
Ladle soup into each of 4 bowls; top with tortilla strips, yogurt, and cheese.