To secure an S rating, defeat three of the four Skulls in the initial battle, then leave the fourth behind. You should then reach Code Talker without being detected. When you leave, the remaining Skull will usually take up position to defend the northern escape route. Avoid this battle by retracing your steps back to the jungle, sprinting past puppet soldiers and calling for a helicopter extraction during the journey. A time of approximately 20 minutes (ideally less) and the boost offered by a Perfect Stealth/No Kills bonus should provide the required rating.