Quick soak (1 hour): Rinse the beans, then place them in a pot. Cover them with water, then bring the water to a boil over high heat. Boil for 1 minute, then remove from the heat and cover. Keep covered for 1 hour, then rinse the beans with cool water.
Long soak (6 to 8 hours): Rinse the pinto beans then place them in a glass bowl and cover them with water. Allow them to soak for 6 to 8 hours to rehydrate (overnight works well).
Rehydrate the ancho peppers
Boil a pot of water.
Halve the ancho peppers lengthwise.
In a pan over medium heat, dry roast the ancho halves (no oil), for 2 minutes per side, using a spatula to place pressure on the chilies to increase skin bubbling on the pepper.
Place the ancho halves into a glass bowl, then pour the boiling water over the halves until the peppers are covered completely.
Soak the anchos for 30 minutes to rehydrate, then use.
Make the sauce
In a saucepan, heat olive oil then sauté the yellow onions until translucent. Add the minced garlic and stir often for 1 minute.
Transfer the onions and garlic to a blender. Add the ancho peppers, tomatoes, all the spices, liquid smoke, cider vinegar, and 1/4 cup water. Blend until the sauce is smooth.
Slow cook the beans
Place the soaked pinto beans, beef stock, and blended ingredients into a slow cooker. Stir to combine.
Set the slow cooker on high and cover. Cook for approximately 2 hours (until the sauce is simmering).
Stir the beans, then recover and set the slow cooker to low. Continue to cook on low for 3 hours.
Add salt, pepper, and additional seasonings to taste, then serve.