A snorkel- these are raised air intakes, also used in very dusty conditions, which when completely sealed stop water entering the air intake.
High level breathers-These are flexible extension lines that fit onto axle and gearbox breathers the open ends of which can be mounted up high. A nice little one way valve on the end works wonders....
Wading plugs-These are threaded plugs that screw into holes in the bottom of the bell housing and flywheel cover to stop water getting onto the clutch, just remove 'em when you're done.
Gas engines need water proofing. Waterproof the ignition and charging systems, remember to keep the engine revs up when in deep water to stop water running back up the exhaust pipe, or baffle the pipe.
A nice electric fan would be nice... so you can cut it off and not destroy your radiator.
I like to have an on-board source of stored air to slightly pressurize crankcased, the distributor and the gas tank... better air bubbling out than water seeping in.
Oh yes, carry lots of WD40 and oil and fluids for changing if something leaks.
Scuba gear if you go deep enough...
A spare alternator, starter and relays kept in a waterproof container.
Weatherpack and grease ALL electrical fittings.
If you're really intent on turning that Jeep into a submarine then install a diesle engine and forget all the bad things that can happen to an ignition system... just be aware that bad things can also happen to a diesel if water enteres the fuel or the engien...bad, really bad things.
Never go in Salt water!