In a large stockpot, over medium to high heat, add water, chicken, 2 teaspoons salt, whole clove garlic, and quartered onion. Cover and simmer for about 30 minutes. Remove the chicken, garlic, and onion from the broth and allow to cool. When the chicken is cool, shred it. Reserve chicken and broth.
In a blender, put the boiled onion and garlic clove, the quartered tomato, chipotle peppers including adobo sauce, 2 teaspoons salt, and enough chicken broth to fill the blender half way. Puree until smooth.
Heat the coconut oil in a large and deep pan over medium heat. Once it is hot but not smoking, stir in the chopped onion and cook until soft and translucent, about 2 minutes. Add chopped tomatoes and chopped garlic and cook for an additional 2 minutes.
Add the shredded chicken, the chipotle sauce from the blender, and more chicken broth if it is too dry. Bring to a boil, reduce heat, and simmer for 20 minutes. Add salt to taste.