In a large heavy-bottomed pot over medium heat, brown ground beef. Drain. Add onion and jalapenos to pot and cook until softened, about seven minutes. Add minced garlic and cook one minute more. then pour in enchilada sauce and diced tomatoes. Juice the lime into the pot, add taco seasoning and all other seasonings. Stir to combine. Increase heat to high until sauce boils, then reduce to low and simmer for two hours (or more, if you have the time).
Cheese Layer
Put cream cheese in a medium bowl and beat on medium speed with hand mixer until loosened. Add Greek yogurt, 1 cup of cotija cheese, salt, garlic powder, and cilantro and beat until combined. Add egg and beat until incorporated. (The remaining cheeses will be sprinkled on top of the cream cheese mixture for the cheese layer.)
Assembly + Baking
Preheat oven to 350 degrees. In the bottom of a lightly greased 9x13 baking pan spread a ladle or two of red sauce. Arrange a layer of tortilla halves to completely cover the sauce. Spread half of cream cheese mixture over tortillas. Sprinkle grated cheddar, pepper jack, and cotija cheese over cream cheese mixture then ladle red sauce over cheese. Repeat. Add one more layer of tortillas and red sauce on top, then sprinkle with cheddar, pepper jack, and cotija.
Cover pan with foil and bake for twenty minutes. Remove foil and bake another 30-35 minutes, or until bubbly and cheese is slightly browned and melty. Remove from oven and let cool at least ten minutes, preferably longer. Serve generous portions topped with avocado slices, freshly chopped cilantro and a squeeze of lime. Keep refrigerated for up to four days. Also freezes well!