Heat the soy sauce, brown sugar, pineapple juice, garlic, and ginger in a pan over low heat. Let the mixture simmer for 5 minutes until the marinade thickens and then let cool.
Cut off the top of the pineapple and carve out a pedestal for the chicken. Save the pineapple top and other pieces for later.
Place the whole pineapple in a casserole dish, stick the chicken on the pineapple pedestal, and coat the chicken with the pineapple marinade.
Place the pineapple lid on top of the chicken and secure the chicken in place with a wooden skewer. Transfer the casserole dish to a preheated oven and cook at 425°F for 15 minutes.
After 15 minutes, remove the casserole dish from the oven and brush another coat of the pineapple marinade over the chicken. Reduce the oven temperature to 375°F, put the casserole dish back in the oven, and cook for another 45 minutes.
Once the chicken has finished cooking, turn off the oven, open the door, and let the meat rest for 10 minutes.
For the citrus avocado salsa, cut up the remaining pineapple and place it in a bowl. Add the red onion, red chili pepper, avocado, and lime juice and mix well.