In a large saucepan over high heat, combine the beans, water and bay leaf. Bring to a boil. Reduce the heat to low, cover partially, and simmer until the beans are tender, 60 to 70 minutes. Drain and discard the bay leaf.
While the beans are cooking, combine the tomatoes, half the yellow onion, half the garlic, the tomato paste, vinegar, chipotle chili, 3/4 teaspoon of the cumin and 1/4 teaspoon of the salt in a small saucepan over medium-high heat. Bring the mixture to a boil. Reduce the heat to medium and simmer uncovered, stirring occasionally, until the liquid is reduced and the mixture is a thick sauce, about 5 minutes. Set the chipotle ketchup aside to cool.
In a frying pan, heat 1/2 tablespoon of the canola oil over medium heat. Add the remaining yellow onion and saute until soft and translucent, about 4 minutes. Add the bell pepper and the remaining garlic and saute until they begin to soften, about 3 minutes. Stir in 1/4 teaspoon of the salt, transfer the mixture to a bowl and let cool. Set the pan aside.
In a food processor, combine the drained beans, onion mixture, brown rice, pecans, green onion, the remaining 1 teaspoon cumin and the remaining 1/2 teaspoon salt. Pulse several times until the mixture is coarsely pureed. Fold in the beaten egg and bread crumbs. Form the mixture into 6 patties, each about 3/4-inch thick.
In the same pan used for the onion mixture, heat the remaining 1 tablespoon canola oil over medium-high heat. Add the patties and cook, turning once, until nicely browned on both sides and heated through, 7 to 9 minutes total.
Serve each burger on a bun topped with 1 tomato slice, 1 onion slice, 1/2 lettuce leaf and a dollop of the ketchup.