Place the thigh meat in a large resealable plastic bag; squeeze the lemon on top and set aside.
Into a food processor with the motor running, drop the garlic and ginger. Add the yellow onion and chile and pulse to chop. Add the yogurt, ketchup, garam masala and 1 tsp. salt; process until smooth. Reserve 1/2 cup of the yogurt mixture and spoon the remaining mixture over the thighs; squeeze out the air and seal the bag. Let stand at room temperature for 1 hour or refrigerate for up to 12 hours.
Thread the thigh meat and red onion pieces onto 12 six-inch-long skewers (about 5 pieces of meat and 2 pieces of onion per skewer).
Preheat a grill to medium. Grill skewers, covered, turning occasionally, until onion is tender and meat is cooked through, 10 to 12 minutes. Sprinkle skewers with cilantro and serve with naan and reserved yogurt sauce.