I have a jeep and have had water up to my feet a number of times without doing anything. When driving in water make a wave in front of your vehicle don't splash or stop once the wave starts. A high intake is great, pre-make one that connects to the TB and goes to your rollcage or someplace high away from splashes, and then when you need it stick it on. Spraying WD40 on parts to prevent water leakage works to some degree as this is what it's made for. I wouldn't worry about raising your exhaust unless you plan to stay submerged for a very long period of time at an idle.

Now once you are done driving through deep water you will want to/need to change all your fluids. Espcialy your diff. fluid. I wuld change them ALL to be safe. You will also need to re-pack your bearings but it's up to you when, but remember water will pull the greese away from the bearings once they heat up and you could fry them. (I`ve had to fix this on the side of the road after my brothers front wheel bearing went out and the rim started scraping on the caliper.)