Cut the roast into 2-inch cubes, and trim excess fat as needed. Season the meat with salt, pepper, cumin and rub it in. Set aside.
Using kitchen shears, cut the tops off the chiles and remove the seeds.
In a large dutch oven on medium heat, add a little oil and fry the chiles for 1-2 minutes per side. Move the chiles constantly so they will not burn.
In a medium bowl, add the fried chiles and 3 cups of boiling water. Let them sit for 10 minutes to allow the chiles to soften.
In the same dutch oven on medium heat, saute the onion and tomatoes until they start to brown, about 5 minutes. Next, add the cloves, thyme, oregano, peppercorns, marjoram, bay leaves, cinnamon stick, and garlic. Continue to cook for 3 minutes, and stir frequently.
Add the chiles (including water) and ingredients from the previous step, cumin, vinegar, salt, and 1 cup of water in a blender. Blend until completely smooth. Strain the sauce through a fine-mesh strainer and set aside.
Using the same dutch oven, add a little more oil, and saute the meat in batches until browned on all sides. It will take about 10 minutes. Add the strained sauce, the remaining 2 cups of water, and cook medium-low heat for 3 hours or until fork-tender.
In a small bowl add the sour cream, minced chipotle pepper and adobo sauce. Mix until completely combined and set a side.
Remove the meat from the dutch oven and shred it using 2 forks. Cook the fries according to package instructions. Serve on top of the fries and add your favorite toppings. We added cilantro, cotija cheese, avocado, pickled onions and jalapenos, and limes.