Peel and/or cut away the dark, fibrous parts of the lemongrass until you get to the white and light green portions. Using a knife, finely chop lemongrass.
In a large bowl, combine vinegar, calamansi juice, garlic, ginger, lemongrass, sugar, salt, and pepper. Whisk until well-blended.
Add chicken and cover bowl. Marinate in the refrigerator for at 2 to 4 hours.
In a wide pan over medium heat, place chicken fat and cook, turning as needed, until crisp and renders oil. Using a slotted spoon, remove skin and bottoms.
Lower heat and add annatto seeds, crushed garlic, and bay leaf. Cook for about 1 to 2 minutes, turning as needed to prevent seeds from burning.
Remove the pan from the heat and allow the oil to steep for about 1 hour or until oil is infused with deep orange color. Using a fine-mesh sieve, strain oil. Discard aromatics and set aside oil.
Lightly grease grill grates and heat over hot coals.
Drain chicken from marinade and scrape off any stray aromatics. Arrange chicken in a single layer over hot grates with skin side up.
Grill chicken, turning once or twice and basting regularly with the half of the chicken oil, for about 30 to 40 minutes or until a thermometer inserted in the thickest part of chicken registers 160 F.
Remove from heat, cover, and allow to rest for about 3 to 5 minutes. Serve hot with the remaining chicken oil and steamed rice.