Well, I think above worrying too much about making them waterproof is that no matter how we try to make Jeeps water resistant, they'll never be waterproof. Water can get into the sensors, inside the connectors, steering column where it seems to be especially sensitive to water (clockspring, turn-signals, instrument panel), etc. Taking it through deep water is really just plain risky. Every couple 'a days, someone posts about their electrical system is hosed, intermittent, clicking, engine running rough, etc. and about all we can say is to let it dry out for a few days and start spraying everything you can get to, electrically speaking, with WD-40 to chase the moisture away.
It's just that water and TJs are a sometimes problematic combination. Some days you'll reach the other side without a problem, others you're gonna stall out and have to be towed out... and give it time, often even a few days, to dry out so all the sensors and other doo-dads can start working again.
But then I'm a desert Jeeper, we have to carry our own water with us and my few water crossings always gave me a minor headache afterwards.