Preheat oven to 400°F.
Place one red onion, the garlic, scallions, lime juice, jalapeño peppers, red wine vinegar, orange juice, paprika, cumin, allspice, cinnamon and thyme in a food processor and pulse to combine. While running, stream in the EVOO to form a thick paste.
Place the chickens in a roasting pan and season generously with salt and pepper. Rub the paste on the chicken and place in the oven to cook until the internal temperature reaches 165°F, about 1 hour.
Place the pineapple, bell peppers and 2 red onions on a baking tray. Season with salt and pepper and drizzle them with some EVOO. Place tray in the oven 30 minutes before the chicken is done cooking.