The best way to water proof a jeep is to keep it in the garage where it belongs. 
I think that phloop is a bit ticked by the use of the word "jeep" interchangably with "Asunna".
No matter what you call it, your Asuuna Sunruner/Geo Tracker/Sidekick,Vitara/etc. is most definitely
NOT a Jeep (a registered Trademark of Chrysler/Daimler or whomever owns Chrysler right now...).
Oh boy, I better shut my pie-hole before I say something stupid on this topic...

On the subject matter at hand.
The most common ways to "waterproof" a 4x4 is to:
Plumb the transmission, transfer case and differential vents with watertight tubing that terminates as high on the vehicle as possible.
Build/install a snorkle that draws air into the engine from a high point on the truck.
After high water crossings, remove and thoroughly dry out your ECM. Alternatively, you can change your intake system so that it no longer needs an ECM. A "stupid" carb swap is a typical method.
If you had a Samurai, you could ship it to Dutton in the UK and have it converted for amphibious use.
I hope that this helps!