Whisk the marinade together. In a medium mixing bowl, whisk together the soy, mirin, honey, ginger, garlic, sesame oil, salt and pepper together until smooth.
Marinate the steak. Toss the cubed sirloin with the marinade until the pieces are well-coated. Cover and transfer to the fridge for at least 2 hours, up to 24.
Assemble the skewers. If you're using wooden skewers, make sure to soak them in cold water for an hour. Thread pieces of steak onto the skewers, alternating with shishito peppers and red onion. Reserve the marinade.
Preheat the grill. Before using your grill, make sure to clean the grates of any food and debris. Lightly grease the grates with nonstick spray. Preheat an outdoor grill to medium-high until the temperature reaches 400 F.
Grill. Lay the skewers on the hot grill and grill for 4-5 minutes per side for medium. As the kabobs grill, brush with the reserved marinade. For more doneness, increase the time on the grill. Remove from the grill and rest for 10 minutes before eating. Top with chopped cilantro and green onions before serving. Serve with a squeeze of fresh lime.