Preheat your oven to 375 degrees F (190 degrees C).
Fill a large pot with lightly-salted water and a three to four drops of olive oil. Bring it to a rolling boil.
Add the pasta, stirring as you do and return to a boil. Cook the pasta uncovered, stirring occasionally, until the pasta has cooked through but is still firm to bite, about 5 minutes.
Drain well and rinse the pasta with cold water to stop it from continuing to cook. Set the shells aside.
Grind the chili pepper, garlic cloves and garlic scapes in a grinder or mortar and pestle.
Heat a large skillet over medium-high heat to cook the ground beef in until it is crumbly, evenly browned, and no longer pink. Drain and rinse the ground beef with hot water to remove any excess grease.
Add the bacon, spices and pasta sauce to the ground beef in the skillet. Bring to a simmer over low heat. Cook for 5 minutes stirring frequently.
Spread half of the sauce into a 9x13-inch baking dish.
Add the cottage cheese, 3/4 of the mozzarella cheese, Parmesan cheese a large mixing bowl and stir to combine well.
Spoon the cheese mixture into the shells and set them into the prepared baking dish on top of the sauce.
Once the shells are filled with the cheese mixture, pour the remaining sauce over the shells and sprinkle with the rest of the mozzarella cheese.
Bake in oven about 30 minutes until the shells are hot in the center and the mozzarella cheese is melted and bubbly.