Preheat oven to 400°F. Butter 9x13-inch baking dish and set aside.
Scatter pumpkin seeds on small, rimmed baking sheet and slide into oven. Toast, shaking pan a few times, for 4 minutes or until seeds are very lightly browned.
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.
Bring large pot of salted water to rolling boil. Cook shells just to al dente and strain.
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.
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.
Bake 35-40 minutes, or until mac and cheese is bubbling vigorously and shell edges are light golden brown. Serve immediately.