yeah, the citric acid in soft drinks will eat rust. If you leave it in too long it will start to eat steel, but this will take a week or more to even start. WD-40 or any of the common rust removers/lubes will remove rust as long as they are not silicone or graphite.

Sealed bearings will help and use some silicone between your outer diff case halves. Plus, make sure you have some grease on your gears as grease will repel water.

I run one of my MT's up past its body in water. I just make sure I have everything silicone sealed, especially the batt/reciever case and diffs. Just toss a piece of pipe on your carb opening for a snorkel lol.