Heat the oven to 425 F. Line a baking sheet with foil. Place acorn squash halves on the baking sheet. Roast for 30 minutes; cover and set aside. Heat a large skillet on medium-high heat. Add the oil and saute apples, shallots, celery, carrots and garlic until tender. Add quinoa, pecans, thyme, salt and pepper to the skillet; mix thoroughly. Stuff each side of the squash with 1/2 cup mixture and bake in the oven for about 5 to 10 minutes until heated through.