Silicone grease. It does wonders. On my Toyota I coat the stuff around my distributor and I also have a rubber cover for it to help seal it up. You can pull the spark plug boots off at the engine and coat the silicone grease around those too. Any spots where you think water might be able to get in, you should probably give it alittle coat of it. Its a bit of a pain to clean up but you don't often need to. That and the snorkel. Add some rubber hosing to your diff vents to get them up higher to help you keep some water out, make sure your axle seals are good to help keep water out as well and also make sure your front mail oil seal is good. Doing all that has pretty much made my Toyota a submarine until I get water in my snorkel or exhaust.
2006 FX4 Level II
31x10.5 Goodyear Wrangler Duratracs, 15x7 DSG Alcoas