How to Make It
Stir together miso, oil, sugar, and fish pepper flakes in a small bowl. Rub mixture all over pork shoulder. Using kitchen twine, tie pork shoulder to shape into a uniform size. Wrap tightly in plastic wrap, and chill 8 hours or overnight.
Preheat oven to 300°F. Arrange onion slices in a single layer in a large cast-iron skillet. Unwrap pork shoulder; place on top of onions. Tent pork with a piece of parchment paper; cover with aluminum foil. Roast 2 hours. Uncover pork, and roast until internal temperature registers 150°F, about 30 minutes.
Toss apples with butter, salt, and black pepper. Scatter apples around pork, and roast until a thermometer inserted in pork registers 180°F and apples are crisp-tender, about 45 minutes, stirring apples halfway through roasting time. (Tent pork with another piece of foil if meat is getting too dark.) Transfer pork to a cutting board, and let rest 10 minutes before slicing. Serve pork with apples and onions.