Broil chilies in oven until skin blackens, turning often. Transfer to paper bag for 5 minutes.
Rub gently to peel the skin. Make a slit the length of each chili, and remove and discard seeds.
To make the salsa roja, roast tomatoes, chili pepper, and onion for 20 minutes at 350oF. Transfer to a blender and process with remaining ingredients.
To make the filling, sauté onion in oil until tender in a large pan. Add the garlic, tomato, corn, lemon juice, salt, pepper, and oregano. Cook for 3-5 minutes longer. Add the quinoa and beans.
Stuff each chili with 1 cup of filling. Bake for 20 minutes at 400°F.
Serve over salsa roja and topped with queso.