Preheat oven to 450°F.
Season pork butt all over with salt and pepper. Stir mustard, sugar, thyme, and red pepper flakes together in a small bowl. Place the pork butt, fat side (the big white cap!) up in a large Dutch oven or other roasting dish (a deep pyrex is fine) and pour the mustard glaze over top. Rub it down the sides of the pork.
Roast for 15 to 20 minutes, until the top is bubbly and golden.
Reduce oven temperature to 325°F.
Take the pork out of the oven and place on the stovetop. Add the onion, garlic, and vinegar around the pork. Put the lid on (or cover tightly with aluminum foil), and cook for 4 1/2 to 5 1/2 hours, turning the pork over in the vinegar every 2 hours. This will become more difficult as it starts to fall apart, that’s OK!
The pork is ready when it shreds EASILY all the way to the center. If you start to shred the pork and it doesn’t fall apart VERY easily, it needs more time!
Use two forks to shred the pork, right in the pot so that it can saturate in the juices. Serve straight from the pot, or transfer to a serving platter.