Pretty interesting ideas you're gathering there. In matters of plots and in order for the investigation to be somewhat confusing in the first part of the adventure I think it's always good to have at least two sets of secretive protagonists in the plot. This way when the players are searching for clues in the disappearance of an archaeologist friend (for instance) they assume there is one evil group active in the area. Only after a while, inconsistencies and contradicting clues will point out that for instance there is both a cult trying to keep a portal/ancient god under control and a secret group of occult power mongers who actively try to cross the threshold/awaken the abomination. If your players are new to CoC, a simple plot can do the trick, and the atmosphere of fear will complete the rest. With experienced players it needs a little more sophistication, maybe be approached at some point of the story by a mad professor and be offered to share tremendous power and join an evil society.
Archaeological remnants of Olmec culture and the creepy jungle around seem very promising for the atmosphere I must say.
Au gibet noir, manchot aimable, dansent, dansent les paladins
Les maigres paladins du diable les squelettes de Saladins.