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.