Preheat oven to 400°.
Cut squash in half lengthwise; discard seeds and stringy pulp. Place squash, cut sides down, in a jelly-roll pan. Cover and bake at 400° for 1 hour or until tender. Cool. Scoop out pulp to equal 3 cups. Place pulp in a blender or food processor; process until smooth.
Combine pureed squash, apple juice, and the remaining ingredients in a large saucepan or Dutch oven; bring to a boil. Reduce heat, and simmer, uncovered, 45 minutes or until thick, stirring frequently. Cool. Store in an airtight container in the refrigerator up to 2 months.