Preheat oven to 400°F.
Heat a skillet over medium-high heat with oil, 2 turns of the pan. Add onions and garlic, and stir 2-3 minutes. Add spices, salt and pepper, and stir 1 minute; add chicken, stock and chipotle, and simmer to combine flavors.
Layer tortillas and chicken in casserole dish, and top with cheese. Bake until brown and bubbly, 12-15 minutes. Top casserole with salsa and pickled jalapeños, and serve with passed sour cream at the table.