In a large saucepan over medium heat, heat the oil, and add the onion; sauté 5 minutes. Add the garlic and sauté until the onion is tender, about 5 minutes. Add the crushed red pepper and sauté 30 seconds. Add the tomatoes. Simmer until the sauce is reduced to 5 cups, stirring occasionally, about 1 hour. Season to taste with salt and pepper. Remove from heat and mix in the fresh basil.
PREPARE THE FILLING:
In a medium bowl, combine the ricotta, 1 1/3 cups of the feta cheese, basil and chives. Season to taste with salt and pepper. Stir in the eggs.
COOK THE PASTA:
Cook the shells in large pot of boiling salted water until just tender but still firm to bite. Drain. Rinse with cold water until cool. Drain thoroughly.
ASSEMBLE AND COOK:
Preheat oven to 350 degrees F.
Spread ¾ cup of sauce in the bottom of each of two 13×9-inch glass baking dishes. Fill 30 shells and divide between the dishes. Top with the remaining sauce and sprinkle with remaining feta.
Bake until the shells are heated through, about 40 minutes. Garnish with additional basil leaves.
Notes
*To save time on cooking day, you may prepare the sauce a day in advance and refrigerate.
*You may also prepare the entire dish a day ahead, cover and refrigerate until ready to bake.