Preheat oven to 300 degrees. Toss together all ingredients and spread mixture in a single layer on a parchment-lined rimmed baking sheet. Bake, stirring every 15 minutes, until seeds are crisp and pulp is caramelized, 50 to 60 minutes. Let cool completely before serving. Squash seeds can be made up to 1 week ahead and stored at room temperature.