Preheat the oven to 400 degrees F.
In a large Dutch oven over medium-high heat, add the oil. Season the short ribs with salt and pepper, to taste. Add short ribs to pan, 1 at a time, and sear on all sides until nicely browned. Remove them from the pan to a platter.
In the same Dutch oven, over medium-high heat, add the onions. Cook until the onions are well caramelized, about 2 to 3 minutes. Add the garlic and mix well. Stir in the chipotles, salsa, stock and salt and pepper, to taste. Bring to a boil, then add the short ribs and cover. Put the pot in the oven and braise the ribs until the meat is fork tender, about 1 1/2 to 2 hours.
Remove the ribs from the oven and shred the meat with 2 forks. Slice the peppers into thin strips and put them in a bowl along with the cilantro. Warm the tortillas in the oven. Assemble the fajitas with the desired amount of short rib meat and top with peppers.
Garnish with lime wedges and serve.