MAKE THE FILLING. In a large bowl, beat the eggs until smooth.
Add the ricotta, mozzarella, pecorino and black pepper and mix until well combined.
Season with salt, to taste.
Transfer the filling to a piping bag fitted with a large round tip and refrigerate until ready to use.
MAKE THE SAUCE. In a medium-sized saucepan, melt the butter over medium-high heat, swirling the pan to avoid browning.
When the butter begins to foam, add the flour and whisk to combine, until completely incorporated.
Slowly drizzle in the milk, whisking constantly, until fully combined.
Cook, stirring often, until the sauce thickens and coats the back of a spoon, about 3 minutes.
Add the pecorino and stir to combine.
Remove from the heat, add the pepper, and season with salt, to taste, whisking to combine.
MAKE THE SHELLS. Bring a large pot of generously salted water to a boil.
Add the shells and cook for the recommended cooking time for baked stuffed shells (usually about 9 minutes), then drain.
Preheat the oven to 350-degrees.
Spread 1 cup of the sauce evenly into the bottom of a 9-x 13-inch baking dish.
Pipe the filling into the shells, using about a scant ¼ cup of filling per shell, placing them into the baking dish when filled.
Spoon the remaining sauce over the shells, being sure to coat each evenly.
Sprinkle the pecorino evenly over the top.
Sprinkle the mozzarella evenly over the top.
Cover tightly with aluminum foil and bake until the sauce is bubbling around the edges and the cheese is melted, about 45 minutes.
Increase the temperature to broil, remove the foil, and cook until the mozzarella begins to caramelize, for 2 to 5 minutes.
Let sit for 5 minutes; to serve, place 2 to 3 stuffed shells onto a serving plate, spoon some of the sauce over the top and garnish with a light sprinkling of pecorino and a crack of freshly ground black pepper.