Put the vinegar, sugar, reserved pineapple juice and cornstarch slurry into a small saucepan. Bring to a boil over medium heat, then reduce heat and simmer until the sauce thickens, about 8 minutes. Remove from heat and set aside. Reserve half of the sauce in a small serving bowl to be used as a dipping sauce alongside the skewers.
Quarter the red pepper and remove the core and seeds. Slice each quarter into 6 pieces. Cut each chicken thigh into 6 pieces.
Preheat a grill pan or an outdoor grill to medium heat.
On each of the 8 skewers, place 1 chunk of pineapple, then a piece of chicken thigh, followed by a piece of red pepper. Repeat with another piece of pineapple then chicken, then red pepper. Season skewers with salt and pepper, to taste. Grill the skewers on oiled grill, cooking for 4 minutes on each side. Brush the sweet and sour sauce all over the skewers and grill and additional 2 minutes per side. Remove to a serving dish and serve with the reserved sweet and sour sauce, for dipping.