Layer chilies on a foiled cover baking sheet. Place chilies 6-8” under broiler until charred all over.
Place charred chilies in a bowl. Cover with plastic wrap and leave covered for 10 minutes.
Reduce oven to 350 degrees
Mix hamburger meat with onions and bell pepper and cook until done. Mix in taco seasoning according to package instructions and simmer for another 10 minutes.
Remove chilies from bowl and peel charred skin from chilies. Discard charred skin.
Spray 8x8 or 9x9 baking dish with non-stick cooking spray. Lay half of the chilies evenly in bottom of baking dish. Cover with half of the beef mixture and sprinkle with half of the Jack and Cheddar cheeses, and cover with remaining chilies and beef mixture.
In a bowl, mix together the eggs, milk, and flour, and pour over the top layer of beef mixture.
Bake in the preheated oven for 25 minutes. Remove from oven, pour enchilada sauce evenly over the top, and continue baking another 15 minutes. Sprinkle with remaining Jack, Cheddar cheeses, tomato, and green onion and serve.