In a medium bowl combine the jalapeno, chili powder, cumin, cheddar cheese, Monterey jack cheese, sour cream, green onion, and cilantro. Season to taste with salt and pepper. Make up to 1 day ahead of time, store covered in the fridge.
Cut a 1-inch wide slit into the thick end of each chicken breast and carefully cut down to the center of the breast to form a pocket. Be careful not to slice all the way through. Fill each pocket with the cheese mixture. Press to seal shut.
Place the flour in a shallow dish. Beat the eggs in a shallow bowl. Place the crushed tortilla chips in a shallow dish. Dredge the chicken lightly with the flour. Coat the chicken with the eggs. Dredge the chicken in the crushed tortilla chips, making sure they adhere well to the surface.
Meanwhile, heat the oil in a large oven-safe skillet pan over medium-high heat. Gently place the chicken in the pan and fry until golden brown on one side, about 4 minutes. Turn the chicken over and place in the oven. Bake for 12 minutes, or until cooked through and 165°F internal temperature. Let rest for 5 minutes before serving.
Notes
Crush tortilla chips in a food processor or place them in a ziptop bag and crush with a mallet or rolling pin until finely ground with some larger pieces still remaining.