For the chicken: Add 1 pound chicken thighs, 1/2 onion, 2 cloves garlic, and 1 teaspoon salt to a pot. Cover with 3 cups water and bring to a boil. Reduce heat and simmer 20 minutes until cooked through.
Remove chicken to a plate and let cool. Reserve broth. Once the chicken is cool enough to handle, shred into bite-sized pieces.
Return shredded chicken along with 1 cup of the reserved broth. Cover and keep warm over low heat.
For the salsa: Toast 2 guajillo chiles in a comal or dry skillet over medium heat 30 seconds-1 minute per side until fragrant, careful not to burn.
Meanwhile, bring a small saucepan of water to a boil. Place toasted chiles in the water, remove from the heat and let soak until very soft, about 15 minutes.
Char 4 tomatoes, 1/2 onion, and 2 cloves garlic directly on the comal until softened and lightly blackened. The garlic will char quicker, remove it when it is golden on all sides.
Transfer the tomatoes and onions to a blender with drained guajillos. Peel the garlic and add it with 1/4 cup of the reserved chicken broth and the teaspoon salt. Blend until smooth.
For the masa boats: Mix masa harina, salt, and warm water until a smooth, pliable dough forms. If it cracks at the edges when you press it, add water a tablespoon at a time.
Form a piece of the dough into the size and shape of a wine cork. Using a tortilla press or your hands, press the dough into a small circle or oval about ¼-inch thick.
Heat the 1/4 cup of lard or oil in a skillet over medium heat. Fry chalupas 2 minutes per side until light golden and just crisp. Drain on a paper towel and sprinkle with salt.
To Serve: Spoon a thin layer of salsa roja onto each chalupa. Top with shredded chicken, diced onion, and cilantro. Queso fresco isn’t traditional, but I like it on top. Serve immediately.