Can't this all be happening inside a show building for Epic / CftBL? I think a voyage deep into the Amazon in an always-night indoor jungle/lagoon with this ride system would be pretty great. If the boats had a Jungle Cruise-like canopy overhead you could go through a tropical storm with rain, plus have wind blowing all the foliage around.
Plus you could have a moment where there is lightning flashing and you see the silhouette of the Creature who has climbed on top of your boat! (It would be a figure suspended from above, essentially from a dry-cleaning track synched with the ride vehicle).