Combine molasses, pickling salt, and water in large container. Add Boston butt making sure it is completely submerged in brine, cover, and let sit in refrigerator for a minimum of 8 hours. 12 hours is ideal.
Place cumin seed, fennel seed, and coriander in a spice grinder and grind fine. Transfer to a small mixing bowl and stir in chili powder, onion powder, and paprika.
Remove Boston butt from brine and pat dry. Sift the rub evenly over the shoulder and then pat onto the meat making sure as much of the rub as possible adheres.
Preheat smoker to 210 degrees F. Place butt in smoker and cook for 10 to12 hours, maintaining a temperature of 210 degrees. Begin checking meat for doneness after 10 hours of cooking time. Use fork to check for doneness. Meat is done when it falls apart easily when pulling with a fork. Once done, remove from pot and set aside to rest for at least 1 hour. Pull meat apart with forks and serve.