Heat a skillet over medium-high heat. Add dried chiles; cook, turning occasionally, until toasted and blistered in spots, 3 to 5 minutes. Add 1 cup water to just cover the chiles, and bring to a simmer over medium-high. Cover and cook, undisturbed, until softened, about 5 minutes. Drain well.

Combine chiles, achiote, garlic, chipotles, 2/3 cup onion, orange juice, vinegar, oil, cumin, brown sugar, and salt in a blender; process until smooth, about 30 seconds. Reserve 1/2 cup marinade, cover, and refrigerate until ready to use.

Place remaining marinade in a shallow dish or large resealable plastic bag, add chicken; toss to evenly coat. Cover chicken with plastic wrap, and refrigerate at least 8 hours or up to 24 hours.

Place wooden skewers in a shallow dish; cover with water by 1 inch. Let stand at room temperature while chicken marinates.

Preheat the oven to 400 degrees F (200 degrees C). Position oven rack 8 inches away from heating element. Line a small roasting pan or 13- x 9-inch baking dish with aluminum foil.

Thread 1 pineapple slice onto 2 skewers, being sure to pierce through the center core, (skewers will be about 1 inch apart), leaving a 1 1/2-inch space from end of skewer. Thread 5 to 6 pieces of marinated chicken, stacking on top of pineapple; thread 1 pineapple slice. Repeat process, ending with pineapple slice, until all chicken pieces and pineapple slices are used, making 4 stacks total. Brush with any remaining marinade from chicken.

Place stacked skewers in the prepared pan, resting skewer ends on edge of pan so that the chicken doesn't touch the bottom of the pan.

Bake in the preheated oven for 30 minutes. Flip skewers over, brush with reserved 1/2 cup marinade. Bake until chicken is no longer pink in the center and the juices run clear, about 30 minutes longer. An instant-read thermometer inserted into the center should read 160 degrees F (71 degrees C). Increase oven temperature to broil; broil until browned and crispy, 3 to 5 minutes. Flip, and broil until browned and crispy, 3 to 5 minutes.

Meanwhile, heat a large skillet over high heat. Working two at a time, add tortillas; cook, turning once, until heated and browning in some spots, 1 to 2 minutes per side. Repeat with remaining tortillas.

Remove chicken and pineapple from skewers, place on cutting board, roughly chop.

Divide chicken and pineapple between heated tortillas; top with remaining onion and cilantro.