In a skillet set over medium- high heat, heat the oil. Cook the onion and red peppers, sautéing for 4 to 5 minutes until the onions have softened. Sea son with salt and pepper and add garlic, cooking for another minute. Stir in the pumpkin puree, stock, jalapeños, chili powder, and nut meg. Taste the sauce and see if you need to add more salt or pepper. (The amount needed will vary depending on the stock used.) Remove sauce from heat.
Pour 2 cups of the pumpkin sauce into the bottom of an oiled 9×13- inch pan. Lay 6 tortillas onto the bottom of the pan, overlapping or tearing some of them in half as needed to fit. Top the tortillas with half each of the black beans, pinto beans, and turkey. Pour 1 cup of pumpkin sauce over the bean layer. Repeat the layers starting with the tortillas, then the beans and turkey, and then another cup of pumpkin sauce. Top with the remaining tortillas. Pour the final amount of pumpkin sauce on top, smoothing as needed to completely cover the tortillas.
Sprinkle with the cheese substitute.
Bake for 45-60 minutes until bubbling.
To freeze:After sprinkling with the cheese substitute, top with a layer of parchment paper, then cover with aluminum foil, sealing well to remove as much air as possible. Label and freeze.
To serve: Thaw. Bake at 350oF for 45-60 minutes or until bubbling.