The night before you cook, pick through each batch of beans, removing any debris or misshapen beans. Rinse the beans put into separate large bowls, and add cold water to cover by at least 2 inches (5 cm). Leave to soak overnight, adding water as needed to keep the beans covered.
The next day, put the guajillo chiles in a bowl, add enough hot water to cover, and leave to soak for 20 minutes. Drain. Carefully slit open the guajillos, and remove the seeds. Put the guajillos and a little soaking liquid in a blender, and puree to a paste. Transfer to a bowl, and set aside.
Drain the beans, and set aside.
Heat a large pot over medium heat. Add the olive oil and onion, and saute, stirring occasionally, until the onion turns translucent, 3 to 5 minutes. Stir in the garlic and saute briefly until fragrant. Stir in the cumin and chile powder.
Stir in the tomato paste, and saute, stirring until it darkens slightly, about 30 seconds. Add the drained soaked beans. Stir in the crushed tomatoes, with their juices, the guajillo puree, salt, and enough vegetable stock to submerge the beans completely. Cover the pot securely and cook, adjusting the heat to maintain a simmer, until the beans are cooked through and tender but still firm and whole, 20 to 30 minutes.
Stir in the quinoa, cover, and cook until tender, 5 to 7 minutes, adding more stock if needed.