Boil jumbo pasta shells according to package directions, minus 1-2 minutes. You want them a little bit undercooked since they'll continue cooking in the oven.
Drain shells and let cool a bit.
Preheat oven to 375 degrees F and spray a 9x13" baking dish with cooking spray. Set aside.
Heat a large skillet over MED heat and brown sausage. Use spatula or potato masher to finely crumble the sausage as it browns.
The last few minutes of cooking the sausage, add onions, green pepper and garlic.
Drain in a colander.
To a mixing bowl, add ricotta cheese, cooked sausage, onions, green pepper, garlic, pepperoni, 1 cup of the mozzarella cheese, Italian seasoning and basil.
Spread about 1/3 cup of the pasta sauce over the bottom of the prepared baking dish.
Use a spoon to fill pasta shells with cheese mixture, then place shells in baking dish.
Top with remaining pasta sauce and sprinkle with final 1 cup of mozzarella cheese.
Add some additional mini pepperoni slices, and sprinkle with a bit of Italian seasoning.
If freezing, at this point, cover tightly and freeze.
Bake for 20-25 minutes, until cheese is melted and bubbling.
Garnish with grated Parmesan and minced fresh herbs.