2) In a food processor puree the onions, garlic, chipotle peppers, jalapeno, tomato puree and sugar and add it to the pot. Increase the heat to medium to steam vegetables a little and sweeten the peppers. Add enough water to cover by 1 inch, about 1 quart, and add tomatoes with their liquid. Bring to a boil and skim off any foam that rises to the surface. Reduce the heat and simmer until the meat is fork-tender and comes apart with no resistance, about 2 hours. As it cooks down, add more water, if necessary. When done, stir in the masa harina.
3) Take a potato masher and mash the chili so the meat comes apart in shreds. Season with salt and pepper, to taste. Garnish each serving with the shredded Cheddar, chives, and sour cream.