Prepare the grill for direct cooking over high heat (450° to 550°F).
Lightly brush the tomatoes, onion pieces, bell pepper, and scallions all over with oil. Brush the cooking grates clean. Grill the vegetables over direct high heat, with the lid closed as much as possible, until they are charred all over and tender, turning as needed. Remove the vegetables from the grill as they are done. The onion and bell pepper will take 10 to 12 minutes, the tomatoes will take 6 to 8 minutes, and the scallions will take 2 to 4 minutes. Place the bell pepper in a bowl and cover with plastic wrap. Let stand for 10 to 15 minutes.
In the bowl of a food processor or blender, process the tomatoes, onion, garlic, chipotle chiles, and lime juice until smooth. Season with salt. Pour the salsa into a glass or stainless steel bowl and set aside.
In a small bowl combine the rub ingredients. Lightly brush the thighs on both sides with oil and season evenly with the rub.
Brush the cooking grates clean. Grill the thighs over direct high heat, with the lid closed as much as possible, until the meat is firm and the juices run clear, 6 to 8 minutes, turning once or twice. Transfer to a cutting board and let cool.
When the thighs are cool enough to handle, cut them into ⅓-inch pieces and put them in a large bowl along with ⅓ cup of the salsa. Remove and discard the stem, skin, and seeds from the bell pepper. Chop the pepper and scallions and add them to the bowl; toss to combine. Season with salt and lime juice.
Heat the tortillas over direct high heat just to soften them, 30 seconds to 1 minute, turning once.
Lay the tortillas in a single layer on a work surface. Evenly divide the cheese and the chicken-vegetable mixture among the tortillas. Fold up the tortillas and serve with the remaining salsa on the side.