Preheat oven to 350F. Grease a 3 quart casserole dish (approximately 13 x 11 inches).
Make the cranberry sauce: In a medium sized sauce pan, combine the cranberries, orange juice, and sugar and bring to a boil. Lower the heat and allow to simmer until cranberries start to pop, approximately 5 minutes.
Saute celery and onion: While the cranberries are cooking, heat 2 tablespoons olive oil in a large pan. Add the diced celery and onion, season with salt and pepper, and saute for about 5 minutes, or until the onions and celery start to soften.
Mix all ingredients in a bowl: In a very large bowl, combine ALL the ingredients: the cranberry mixture, onion-celery mixture, cubed butternut squash, broth, fresh thyme and sage. Mix well. Add the bread cubes and stir just to combine. Top with pecans.
Cover and bake: Transfer to the greased casserole dish, top with chopped pecans, and cover with foil. Bake at 350F for 40 minutes, then remove foil and continue baking for another 20 minutes, or until the butternut squash cubes are fully cooked and fork-tender. Remove from heat , garnish with fresh thyme, and allow to cool for at least 5 minutes before serving.