Trim the roast of any excess fat, and cut into four pieces. Rub with black pepper, and place into a slow cooker. Add the onions, green chiles, chili powder, cayenne pepper, garlic powder, cumin, chipotle peppers, and beef bouillon. Pour in enough water to cover 1/3 of the roast.
Cover, and cook on High until the meat begins to fall apart, about 8 hours. Add water if needed to keep the roast from drying out.
Turn the slow cooker to Low, and remove meat to a large bowl with a slotted spoon. Shred the meat into bite-sized pieces using two forks. Return the meat to the slow cooker; cook about 20 minutes to reheat before serving.