Think in terms of what you plan on doing with the rover. Then move toward upgrading the systems needed to make that sort of driving better while planning through the changes.
Enjoy cruising the beaches and riding with friends - upgrade the electrical system to handle the improved stereo and night driving lights. Then start with the mods.
Lots of slow off-road driving in hot weather Florida - upgrade the cooling system.
This way what is first being addressed are the weak points that will undoubtedly crop up when doing your favorite thing. You are also building a truck to fit your needs. A lot of folks will say something like lift it and run 36" MTR's. But by focusing on popular upgrades having mostly visual value, you are only building a truck that would meet someone else's expectations of what a Rover should look like.
"Uhh...I think they all leak like that."