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Preheat oven to 400°F. Butter a 9 x 13-inch baking dish and set aside.
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Scatter pumpkin seeds on small, rimmed baking sheet and slide into oven. Toast, shaking pan a few times, 4 minutes or until seeds are very lightly browned.
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In bowl of food processor, pulse to combine toasted pumpkin seeds, kale, garlic, lemon zest, 1/2 teaspoon sea salt and 1/4 teaspoon black pepper. With food processor running, drizzle in olive oil until mixture is well combined.
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Bring large pot of salted water to rolling boil. Cook shells just to al dente and strain.
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In heavy-bottomed saucepan, melt butter over medium heat. Whisk in flour and 1/2 teaspoon sea salt, and cook, stirring often, for 2 minutes. Slowly whisk in milk, 1/4 cup at a time, waiting until milk is fully incorporated and mixture thickens before adding more. Once all milk has been added, turn off heat and fold in fontina, asiago, and 1/2 cup parmesan.
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Pour cheese sauce over shells and stir to combine. Spoon into prepared baking pan. Dot shells with pesto, swirling pesto in with spoon. Top with remaining 1/4 cup shredded parmesan and a 1/4 teaspoon ground black pepper.
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Bake 35 - 40 minutes, or until mac and cheese is bubbling vigorously and shell edges are light golden brown. Serve immediately.