Split whole chilies lengthwise; remove seeds and lay flat in a 13x9 inch baking pan. Place tofu on paper towels and press gently to remove excess moisture. Crumble tofu and blend half of it with the cheddar cheese and half of the tofu with the jack cheese. Top whole chilies with half of cheddar cheese mixture and half of the jack cheese mixture. Add a layer of the diced chilies.
Repeat layers of cheeses and chilies. Beat eggs with milk and pour over all. Spread with salsa. Bake in 350 degree oven for 45 minutes.