Heat the oil in a large saute pan over medium-high heat. Add the onions and saute until they begin to soften, about 3 minutes. Add the chipotles, garlic, cumin, salt and cayenne and saute until fragrant, about 1 minute. Stir in the tomatoes and stock and cook until they begin to simmer, about 2 minutes. Turn off the heat and carefully ladle the sauce into a heat-safe blender. Puree until smooth. Pour the sauce back into the pan over medium heat and add the chicken, stirring to incorporate the chicken into the sauce. Cook until the sauce has thickened, about 5 minutes. Serve with tortillas and desired toppings.
Pickled Shallots and Red Onions:
Combine the white vinegar, sugar and 1 teaspoon salt in a small saucepan with 1/2 cup water. Bring to a simmer over medium-high heat. Add the onions and shallots to a pint jar and pour the liquid over the top. Let cool completely. Refrigerate up to 1 week.
When blending hot liquid, first let it cool for five minutes or so, then transfer it to a blender, filling only halfway. Put the lid on, leaving one corner open. Cover the lid with a kitchen towel to catch splatters, and pulse until smooth.