Place the beef in a 6- to 8-quart slow cooker. Season with salt and pepper. Arrange the yuca, squash and Cubanelle pepper around the beef in a single layer. Combine the tomato sauce, 1/2 cup water, the cilantro stems, garlic, oregano, 1/2 teaspoon salt and a few grinds of pepper in a small bowl. Pour all over the meat and vegetables. Cover and cook on low until the meat is tender and easy to pull apart, 8 hours.
Meanwhile, thinly slice the red onion. Bring the vinegar, 1/2 cup water and 1/2 teaspoon salt to a boil in a small saucepan. Remove from the heat and stir in the red onion, submerging the slices. Let cool, then transfer to a bowl and refrigerate until ready to serve.
Remove the meat to a plate and shred into bite-size chunks with 2 forks, discarding any large pieces of fat. Skim off any excess fat from the remaining stew in the slow cooker. Stir the meat back into the stew and season with salt and pepper. Divide among bowls. Top with the chopped cilantro leaves. Drain the pickled red onion and serve with the stew.