Carefully slit each pepper lengthwise along the center about ½ to ¾ of the way down, remove seeds and veins. Fill each pepper with several strips of cheese, roll in the flour, and set aside.
Beat the egg yolks in a small bowl, stir in the baking powder. Set aside. In a large bowl, beat the egg whites until they form stiff peaks (best to use an electric mixer for this); gently fold in the egg yolk mixture.
Pour oil into a frying pan to the depth of 1 inch; heat to 400 °F. Take a chile and roll it in the egg batter, gently lay, seam side up, in the hot oil to cook. Cook until brown, then gently turn, cook the other side. Drain briefly on paper towels to drain.
Prepare the Sauce: In a skillet heat the oil over medium heat; add the onions and jalapeño; sauté until the onion is soft, about 5 minutes; add the garlic, cook 1 minute more; add the tomatoes and chicken stock, bring to a simmer and simmer for about 15 minutes.
Lay the relleno into the sauce and simmer for just a few minutes (do not cook too long or the coating will separate and get very soggy); turn to coat. Place relleno on plate and spoon sauce over. Serve immediately. Top with optional ingredients, if desired.