Place chicken drumsticks and thighs in a large bowl, and season with 1 teaspoon salt and ground pepper; set aside.

Cut 1 garlic head in half crosswise. Peel cloves from remaining garlic head, and set aside. Combine halved garlic head, 3 quarts water, cilantro bunch, spearmint bunch, scallions, 2 onion halves, 2 teaspoons black peppercorns, 2 teaspoons allspice, and 1 tablespoon salt in a large stockpot. Bring to a boil over medium-high. Reduce heat to medium-low, and simmer 20 minutes.

Add chicken to pot; return to a boil over high. Reduce heat to low, cover, and simmer, skimming off and discarding foam occasionally, until chicken is tender but not falling apart, about 30 minutes. Remove chicken pieces with a slotted spoon, and transfer to a large bowl; cover with plastic wrap until ready to use. Pour broth through a fine wire-mesh strainer into a bowl (you should have about 9 cups of broth); discard solids. Wipe stockpot clean, and return strained broth to pot; set aside.

Heat a large cast-iron skillet over medium-high 2 minutes. Reduce heat to medium; add cinnamon stick, remaining 1 teaspoon peppercorns, and remaining 1 teaspoon allspice. Cook, stirring constantly, until fragrant, about 15 seconds. Transfer to plate; let cool 5 minutes. Add pepitas and sesame seeds to skillet; cook, stirring constantly, until lightly toasted, about 40 seconds. Transfer to a plate; let cool 5 minutes. Process cinnamon mixture in a spice grinder until finely ground, about 15 seconds; transfer to a small bowl. Working in batches, add pepita mixture to spice grinder, and process until finely ground, about 15 seconds. Transfer to a separate small bowl.

Add half of the tomatoes, half of the tomatillos, and 1 onion half to skillet. Cook over medium-high, turning occasionally, until lightly charred, about 10 minutes. Transfer tomato mixture to a blender. Repeat with remaining tomatoes, remaining tomatillos, and remaining onion half. Add roasted bell pepper, peeled garlic cloves, and ground cinnamon mixture to blender. Process on low speed, gradually increasing speed to high, until mixture is smooth, about 40 seconds.

Stir tomato mixture into strained chicken broth in pot. Bring to a boil over high. Reduce heat to medium, and simmer, stirring occasionally, until flavors meld, about 30 minutes.

Meanwhile, whisk together achiote paste and 1/4 cup simmering broth mixture in a small bowl until blended and smooth. Whisk achiote mixture and ground pepita mixture into simmering broth in pot. Return to a simmer over medium. Cook, stirring occasionally, until stew has thickened slightly to the consistency of heavy cream, about 30 minutes. Stir in remaining 1/4 teaspoon salt. Gently return cooked chicken pieces to stew. Increase heat to medium-high, and cook until warmed through, about 5 minutes.

Make the Chile-Cacao Spice Mix: Heat a large cast-iron skillet over medium-high. Add chiles; cook, stirring constantly, until slightly toasted, about 15 seconds. Transfer to a large plate. Add cacao nibs to skillet; cook, stirring often, until darkened and fragrant, about 1 minute. Transfer to plate with chiles; sprinkle with salt and, if desired, pimentón. Let cool 20 minutes. Working in 3 batches, process chile mixture in a spice grinder until finely ground, about 10 seconds. (Do not over-process or the cacao will start to melt and become sticky.) Transfer to an airtight container.

To serve, divide chicken pieces among 6 serving bowls; ladle stew over chicken. Garnish with chopped cilantro and mint. Serve with chile-cacao spice mix, tortillas, and rice.