Preheat oven to 375°.
Roast peppers over gas stove range, for 5 minutes, rotating so all sides char. Remove the blackend peppers from the stove and place in a large resealable bag. Seal the bag and let sit for 15 minutes.
Meanwhile, in a large skillet over medium heat, saute the onion and chorizo for 7-8 minutes, or until the chorizo is cooked through and the onions are translucent.
Remove the peppers from the bag and using a paper towel or washcloth, rub the skins off the peppers. Cut the peppers open and remove the stem and seeds.
Layer the peppers in a sprayed 9x13 pan. Top with the chorizo mixture and crumbled Cojito cheese.
In a large bowl, wisk the eggs with the milk. Pour the egg mixture over the chorizo. Top with shredded Manchego cheese and cover.
Bake at 375° for 45 minutes covered. Uncover and bake an additional 30-40 minutes until the eggs in the middle are mostly set and the edges are golden brown. Allow to sit 5-10 minutes before serving.
Serve garnished with cherry tomatoes and cilantro.