Preheat the oven to 375°F (190°C) and spray a 9×13-inch baking dish with nonstick cooking spray.
Bring a large pot of salted water to a boil and cook the jumbo pasta shells according to package directions until al dente; drain and let cool until easy to handle.
In a 12-inch skillet over medium-high heat, cook the ground beef until no longer pink; drain excess grease.
Add the 1-ounce package of taco seasoning, 1/2 cup of the salsa, and 1/4 cup water to the cooked beef; simmer about 5 minutes until the liquid is mostly absorbed, then remove from heat and cool slightly.
In a large mixing bowl, combine the cottage cheese, large egg, and half of the shredded cheddar and pepper jack cheeses.
Stir the seasoned beef into the cheese and cottage cheese mixture until evenly combined.
In a small bowl, mix the enchilada sauce with the remaining 1/2 cup salsa, then spread a little of this sauce mixture in the bottom of the prepared baking dish.
Spoon the meat-and-cheese filling into each cooled shell and place the stuffed shells in a single layer in the baking dish.
Pour the remaining enchilada-salsa mixture evenly over the shells and sprinkle the remaining shredded cheddar and pepper jack cheeses on top.
Bake uncovered for 25 to 35 minutes until bubbly and the cheese is melted; remove from oven and garnish as desired with fresh cilantro or green onions.
