Looks absolutely awesome. I live on a lake so I appreciate the ability to go home and cast a fly or any rod once I get home to take my mind back to reality.

As for the overall suggestions I really can't see the need for gears out of the gate. Since the water has so many rocks (Assuming they are large 12" plus) I would consider maybe a skid for the engine and oil.

2 feet is about the door hieght so I'd suggest the TF BB or the rough country with 2.2 shocks. Both great kits. I have the 2 1/2" but plan to upgrade out of shortly.

I was also thinking tow straps and recovery gear along with a winch and hi-lift. remember that with the force of the water you will be pulling a much heavier load on those 2 or 3 times a year if the river get's you. I'd suggest getting into the 9K class or higher.

 

Here's an idea. Build a small garage next to the river and store your old clunker (Discovery) in it and use it when things are flooding.

 

Thought it needed a bit more emphasis

 

I think you need to decide on your starting and possibly future tire size first, since that will influence lift.

Then make sure you pick the lift that best fits your needs.
The suspension lift kit alone will impact your JK driving pleasure on and off road more than any other mod.
It can also start a chain reaction of other required modifications.

Then think about power: Gears, Flaspaq, CAI, exhaust, etc

Finally focus on all the peripheral gear needed for the river.

Unlike many, you have a specific purpose for your JK, so if you follow a systematic approach you will be happy with your build.