Preheat a grill for indirect and direct cooking at medium heat. For gas grills (with 3 or more burners), turn all the burners to medium-high heat; after about 15 minutes turn off one of the middle burners and turn the remaining burners down to medium. For charcoal grills, bank one chimney starter-full of lit and ashed-over charcoal briquettes to one side of the grill. Set up a drip pan on the other side to avoid flare-ups. (Be sure to consult the grill manufacturer's guide for best results.)
Halve the onions through the root and peel. Cut one half into two wedges. Slice the remaining onion half into 1/8-inch half-moons and reserve for pickling. Drizzle the tomato halves and onion wedges with vegetable oil and season with salt and pepper. Grill the tomato and onion wedges on the hot side of the grill, covered, until dark grill marks appear, about 5 minutes per side.
Place the grilled tomato and onion in a food processor, along with the 1/4 cup vegetable oil, chopped cilantro, smoked paprika, brown sugar, cumin, oregano, garlic, chipotle peppers, 1 tablespoon cider vinegar, 2 teaspoons salt and 1/2 teaspoon black pepper. Blend until smooth. Transfer to a large bowl and add the beef chunks. Toss to coat.
Lay out a large double-layered sheet of extra-wide heavy-duty foil. Put the beef in the center. (If using regular-width foil, divide the beef into 2 foil packets.) Bring the short ends of the foil together and fold twice to seal; fold in the other sides to seal, leaving room for steam. Place on the indirect side of the grill and cover. Cook until the meat is tender and shreddable, 2 1/2 to 3 hours.
Meanwhile, combine 3/4 cup cider vinegar, 3/4 cup water and 1 1/2 teaspoons salt in a small saucepan over medium-high heat. When the liquid comes to a boil, stir in the reserved sliced onions and turn off the heat. Let cool completely and refrigerate until ready to use.
Shred the beef and return to the sauce; toss well to coat. Serve with warm grilled tortillas, pickled red onions, and other desired toppings.
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