1. Preheat oven to 350°F. Cook pasta according to package directions until al dente. Drain, place in a bowl, and stir in marinara sauce. Let cool 10 minutes.
2. Stir in 1½ cup grated mozzarella. Blend cottage cheese, eggs, Parmesan, salt, and pepper in blender or food processor until smooth Line cups of two 8-cup muffin pans with two paper liners each. Place pepperoni or salami in the bottom of each liner. Fill cups half full of macaroni mixture. Carefully pour cottage cheese and eggs over macaroni to fill in gaps. Top with the remaining mozzarella cheese.
3. Bake 20 minutes, until egg is set and tops are puffed and golden brown. Mini pizzas will keep in refrigerator up to 5 days.