I've always understood Whey Foundation as more of an archeological organization and FOF is more of a secret government installation. Both operate independent of each other. The US Government discovered an alien saucer in the middle of the jungle and are doing their own research independent of Whey.There was a point where I would have agreed, but I've come around. When the main gathering area is designed to be the main camping point for the Whey Foundation, so to mix that Whey Foundation with now a military instillation muddles the lore more. How do you explain why they are there, do you change the Whey Foundation to be a cover now, do you take something somewhat grounded and add a mystical element with the temples and aliens/military.
BLSC is the FAR easier refurb IMO. Change the Mini Coopers into Jeeps, and put as many fake trees as possible. Now it becomes an expedition from the base camp into unexplored depths of the jungle mountain side. The MCBR/Scene can be dethemed from the helicopter attack to an ape attack showing that they have gained intelligence and the ability to defend themselves (I know that sounds Planet of the Apes like - I just watched the movie last night) and that's what's happening in the thicket of the jungle. I would do some theme elements in the tunnels to make it really think jungle tree themed and bring back the splash at the end to be crossing a river to get back to base camp.
Retheming Stunt Coaster requires a lot more money. They need to add new shells to the trains. They need to invest in foliage or a facade to cover the shipping crates and the parking deck, take down the billboards, remove the police cars and replace them with different scenery, add an expensive animatronic that'll probably be broken in 5 or so years, and possibly redo the whole helicopter show scene altogether. In contrast if I were to retheme FOF, I would add barbed wire fencing surrounding the ride, maybe a guard shack at the entrance to the portal, and a few "secret government facility Keep Out" signs along the fencing and maybe on the building itself. Change the area audio to something similar to Area 72 at KI.