Put the flour and salt in a large bowl and make a well in the center with your hands. Put the eggs in the center of the well and gently incorporate the eggs into the flour by pulling the flour into the eggs. Dust a clean working surface with flour, remove the dough from the bowl and knead for approximately 5 minutes, until the dough becomes smooth. Shape the dough into a disk, and wrap in plastic wrap and put in the refrigerator for 30 minutes, maximum 48 hours.
Put a large pot of salted water over high heat and bring to a boil.
Dust a clean working surface with flour, remove the dough from the refrigerator, divide into 5 equal pieces and cover with plastic wrap to prevent the dough from drying out. Using a pasta machine, roll each piece of dough out into long thin pieces, adjusting the dial for desired thickness. Put the pasta on a tray and dust with flour. Repeat with the remaining dough, dusting the pasta with flour in between layers to prevent them from sticking to one another. Trim the sheets to fit the baking dish, if necessary.
Put the remaining olive oil on a large baking sheet. Cook the pasta in salted water, gently remove and put on a tray, cover in oil to prevent the pasta from sticking and set aside.
Preheat the oven to 400 degrees F.
Put the squash in a bowl, coat with 1 tablespoon olive oil and season with salt, and pepper. Roast the squash in the oven for approximately 45 minutes, until the squash has become tender and caramelized, turning over half way through cooking. Remove from the oven, put in a large bowl, mash slightly and set aside.
Heat the remaining olive oil in a saute pan over medium-high heat, add the onions and garlic and saute until golden brown. Add the butter and allow to melt. Add the sage, stir, remove from heat. Add to the roasted squash, season with salt, and pepper, gently fold and set aside.
Melt the butter in a small pot over medium heat. Add the flour, stir with a wooden spoon incorporating the flour into the butter until a paste consistency is achieved. Add the milk slowly and stir to incorporate, removing all the lumps. Once the mixture thickens, add the mashed jalapeno and season with salt and set aside.
Preheat the oven to 350 degrees F, and oil a 9 by 13-inch baking dish.
Layer the tomatoes, sheets of homemade pasta, jalapeno bechamel, chopped rapini (broccoli rabe), roasted squash filling, ricotta, and then sprinkle with Parmesan. Finish with a layer of jalapeno bechamel and put whole sage leaves on top, submerging them in sauce. Bake in the oven for approximately 30 minutes, then broil for an additional 5 minutes until jalapeno bechamel becomes golden brown. Serve with Charred Rapini
Put honey in a small pot over low heat, once the honey achieves a thin consistency, add the chile flakes, stir and remove from the heat. Add the white wine and set aside.
Preheat a grill.
In a bowl, lightly toss the rapini (broccoli rabe), cipollini onions, garlic, and olive oil. Put the rapini and onions on a grill, turning over to ensure all sides are charred. Remove from the grill, put in a serving dish, garnish with toasted walnuts and drizzle chile honey.