On the alternator... The water itself wont hurt it... you drive in the rain dont you? Ever driven through a deep puddle.. its really just a rotor in a coil... nothing special(other than the voltage regulator, which you could keep a spare on hand, they are easy enough to R&R)....
Anyway, keep some CLEAN(doesnt have to be potable water), and after the water crossing, RINSE IT WELL. the MUD, and silt, dirt, etc, will wreak havoc on the bearings, and cook onto the windings, etc....
I do not advocate deep water crossings... just stating what I have discovered...
IF, you REALLY wanted to have an extreme alternator, a few years of Caddy Northstar used a liquid cooled alternator... cooled by the coolant... should be plenty easy to plumb into your system...
NOW, yes dieletric grease will help. You have factory "weather pack" connectors, which really are pretty good.. but, the grease is always a good thing...
Use it on all electrical connectors, spark plugs, etc. Check, double, and triple check your ignition system, for cracked/damaged plug wires, plugs, etc.. You are more likely to have a problem there, and stall the motor, than any other electrical problem.
Make sure your exhuast is good to go....as long as its running, the engine should provide enough pressure to keep water out.. but, if you stall the motor... its done... water will immediately enter the exhaust, preventing you from starting... Look to the Humvee for ideas on how to deal with that if you wish.
You will have vents/drains in your floor.. so, water will eventually come in...
Move the ECM, and any low wiring, grease....
Use Marine Grade grease in all your fittings... its thick BLUE stuff... Use some kind of dressing on your door seals to make sure they are nice and pliable....
And with the vents for the trans etc... route them into the airbox...
Chase