1. Soak beans in water to cover by 2 inches in large saucepan overnight. Drain.
2. Heat cast-iron skillet over medium-low heat. Remove stems and seeds from pasilla chiles. Toast chiles, turning, until fragrant and pliable, 2 minutes. Transfer to blender with 1/2 cup boiling water; puree. Set aside. Puree chipotles in adobo in clean blender until smooth. Reserve 2 tablespoons; refrigerate remaining for other use.
3. Heat oil in large Dutch oven over medium-high heat. Add onions and bell peppers; cook 10 minutes. Stir in cumin, garlic, and serrano chiles; cook 30 seconds. Add drained beans, pasilla puree, reserved chipotle-in-adobo puree, and 6-1/2 cups water. Bring to boil; reduce heat. Cover and simmer until almost tender, 1 hour.
4. Stir in tomatoes and their liquid, squash, and salt. Return to boil; reduce heat. Cover and cook 10 minutes. Add lima beans and cook 20 minutes more. Remove serrano chiles. Serve with dollops of yogurt, lime wedges, and tortillas. Makes 15 cups.