Place bacon in a large skillet over medium high heat. Cook until bacon is desired crispness, about 10-15 minutes. With a slotted spoon, remove bacon to drain on a paper towel. Pour out all but 1/4 c. bacon grease. Reduce heat to medium; stir the flour into the remaining bacon grease and cook for 2 minutes. Slowly whisk in the milk and pepper. Cook, stirring constantly, until thickened. Remove from heat. Stir bacon into the gravy.
Meanwhile, melt butter in a second skillet over medium heat. Add the onion, red pepper, garlic and crushed red pepper flakes. Cook for 5 minutes, until onions are translucent. Add the mushrooms and continue cooking for 5 more minutes. In a small bowl, whisk together the eggs and 1/4 c. milk. Pour into the skillet, season to taste with salt and pepper and scramble until fully cooked.
Split cooked biscuits and place on individual serving plates. Spoon eggs on top and cover with gravy. Sprinkle with some shredded cheese, if desired.
