Tear Pasilla and Nueva peppers into smaller pieces and toast in a saute pan over medium heat for 3-5 minutes.
Place toasted peppers in bowl with golden raisins, and pour almost bowling water over them. Let rest while preparing the other sauce elements.
Toast thyme, black pepper, cinnamon stick, coriander, and almonds in a saute pan over medium heat for a few minutes until fragrant. Place fragrant mixture into coffee grinder (might need to do this in two batches) and grind into a fine powder.
Then heat oil in saute pan at medium heat and add onions, garlic, and Serrano peppers.
Once the onions are looking brown, add the chopped tomatoes and cook for 30-45 minutes stirring occasionally. The tomatoes will darken in color and become soft.
De-glaze the pan with 1/2 cup of orange juice and 1/2 cup of reserved tomato juice- cook for 10 minutes more. The mixture should look jammy.
Turn off the heat. Drain the peppers/raisins (reserve liquid) and add to pan. Add the ground spices and chocolate. Stir to combine.
Place half of the mixture into a blender with 1 cup of reserved soaking liquid and 1 cup of orange juice. Blend until smooth. Repeat with other half.
Store sauce in an airtight container. This recipe makes a ton of sauce, my thought is if you are going through the trouble of making it, might as well make a big batch because it freezes very well.
Preheat oven to 350 degrees.
Put chicken thighs in a large baking dish so they can lay next to each other in a single layer. Add orange juice and stock to cover chicken most of the way, it's okay if the thighs aren't completely covered. Cover pan with aluminum foil. Bake for 1 hour.
Remove pan from oven and take thighs out of liquid (reserve liquid) . Let cool long enough for you to be able to handle. Pull chicken apart.
Heat 1/2 of mole sauce from recipe above in a saute pan at medium heat. Add chicken and 1 cup of reserved cooking liquid. Simmer for 10 minutes.
Serve over rice or in flour tortillas. Thinly sliced radishes compliment the dish well.