Preheat oven to 450 degrees F.
Slice a thin layer of the bottom of the peppers and the tops as well.
Remove seeds and membrane, then rinse.
Season with salt and pepper and bake for 20 minutes.
While the peppers cook, heat some oil in a large skillet.
Add the onions and mushrooms, cook for 2-3 minutes.
Stir in the garlic and red crushed pepper flakes and cook until fragrant.
Remove the onion mixture and add more oil if needed.
Add the ground beef and break it up with a wooden spoon.
Cook the beef until completely browned.
Add the onion mixture, cumin, oregano, paprika, chili powder, green chilies, 3/4 cup salsa, salt, and pepper.
Simmer the beef over low heat for 25 minutes or until fork tender.
Add rice to the cooked beef mixture.
Stuff peppers with beef and rice mixture.
Pour remaining salsa over the peppers and top off with cheddar cheese.
Bake for 15 minutes and serve with fresh lime.