Pat the short ribs completely dry with a paper towel. Season them all over liberally with salt and pepper.
Heat a large dutch oven over medium-high heat - or use your slow cooker on the saute setting if you have one. Add the oil. Add the short ribs in a single layer and sear on both sides until deeply golden brown, about 3 to 4 minutes per side.
Transfer the short ribs to your slow cooker (or keep them in there if you sauteed them in the crock). Pour in ½ cup of beef stock - keep the remaining ½ cup for the sauce. Cook on low for 6 to 8 hours, until the short ribs are falling off the bone.
Once finished, remove the bones and pull apart the beef with two forks. If your slow cooker has the saute setting, turn it to the highest heat. You don’t need any oil or anything extra, just use what is in the crock. If you transfer to a dutch oven, you will need a drizzle of oil and heat over medium heat.
Once the pot (or slow cooker) is hot, stir in the diced onions and carrots with a sprinkle of salt. Cook until softened, about 5 to 6 minutes. Stir in the garlic and cook for 1 minute. Add in the rest wine to deglaze the pan.
Add the pulled short ribs to the vegetables. Stir in the tomatoes and the remaining beef stock. Bring the mixture to a boil then reduce it to a simmer. Simmer for 15 minutes uncovered, then cover and simmer for 15 minutes more.
Preheat the oven to 350 degrees F. Make the shell filling and follow the directions below.