Most people have done no waterproofing work at all. A few people (the smart ones, a group I don't belong to,) have extended the diff, t-case and transmission breather tubes up to "higher ground."
I wouldn't go any deeper than about halfway up the headlights (if you were standing still in the water, not creating a wake.)
The goal is to keep moving at a fair pace (not fast, but don't crawl through either) so you create a slight bow wave. This will help keep water away from the air intake. Also if you stop in water (or soupy mud) the automatic tranny has a tendency to take a drink. At least one and probably more people here have first hand experience with this.
The most important thing to remember when doing water crossings is NEVER cross fast moving water, even if it is less than a foot deep, and never enter a body of water whose depth you don't know.
A good rule of thumb is if you wouldn't feel comfortable walking through it, don't drive through it.
All that aside, watter crossings are extremely fun and make for awesome pictures! Have fun!
