Vegetables: Using a large stock pot, add the water and vegetables and bring to a boil over medium heat (do not add the rice and beans yet). Keep and eye on the water level to ensure it does not evaporate too much (add water one cup at a time as needed)
Soup Base: Cut or tear the guallijo and arbol peppers down the middle to remove and discard the seeds and stems.
Place the chiles, tomatoes, cloves, bay leaves, and all of the other seasonings and spices into a separate stockpot and cover with about 3-4 cups of water. Bring the mixture to a rapid boil for 10 minutes. Remove the pot from the heat and allow it to cool to room temperature.
Using tongs or a slotted spoon, carefully remove the bay leaves (reserve the water to use later). Add the peppers (and tomatoes if they didn’t dissolve), into a blender with about 1 cup of the cooking water.
Blend on high for 1-2 minutes, or until the mixture is completely pulverized. Using a fine mesh strainer, strain the chile mixture into the stockpot with the vegetables by pushing it around the strainer with a spoon. Add a little bit at a time, until all of the chile mixture is used.
Add the cooking water (and 3-4 cups additional water) to the fine mesh strainer and continue pushing it through with a spoon. This is to ensure all of the flavors are extracted from the chile mixture. The chile mixture will look really dried-up once the flavor is extracted from the straining.
Squeeze the juice of the limes into the soup. Now add the rice and the black beans as well. Continue to heat over medium on the stove top for about 5-7 minutes.
Top with tortilla strips, cilantro, onion, and sour cream if desired.
Notes
Chayote squash is recommended because it keeps the texture. Zucchini or yellow squash can be used as well.