Make sauce: Saute chopped onion and red pepper in 1 tablespoon oil; add tomatoes and all remaining sauce ingredients. Cook 15 minutes over low heat.
Preheat oven to 350 degrees F. Place tortillas on the bottom of a large oiled casserole dish (try not to overlap). Cover each tortilla with Mole sauce. Crack and put one egg on top of each sauce-covered tortilla. Cover with shredded cheese and bake for 30 minutes.