1 teaspoon fennel seeds
1 teaspoon whole black peppercorns
1/4 cup kosher salt
1/4 cup sugar
1 7–8-lb. skinless bone-in pork shoulder (Boston butt or picnic)
1/4 cup apple cider vinegar
1/4 cup (packed) light brown sugar
Salt and freshly ground black pepper
Crush fennel seeds and peppercorns with the bottom of a heavy skillet, or use a mortar and pestle. Transfer spices to a small bowl; add 1/4 cup salt and sugar. Rub mixture all over shoulder. Place in a large glass baking dish, cover, and refrigerate for at least 6 hours or preferably overnight.Preheat oven to 325°.
Brush off spice rub from meat and place pork in a deep roasting pan; discard excess spice rub and any liquid in dish. Add 1 cup boiling water to Dutch Oven, cover tightly.
Transfer pan to oven and roast until meat is very tender and falling off the bone (an instant-read thermometer inserted into the center without touching the bone will read 195°), about 5 1/2 hours.
Remove pan from oven, deglaze with a little water if necessary. Increase heat to 500°. Stir 1/4 cup vinegar and brown sugar into juices in pan. Return to oven and roast, watching closely to prevent burning, until pork is browned and liquid begins to reduce, about 12 minutes.
Transfer pork to a rimmed baking sheet; set aside. Pour liquid in pan into a small saucepan. Bring liquid to a boil and cook, occasionally spooning off fat from surface, until a thick, syrupy glaze forms, about 10 minutes (there will be about 1 1/2 cups glaze and up to 1 cup fat; discard fat). Season glaze with salt and pepper; set aside.
To serve: pour reserved liquid over pork.