General consensus is that the only thing that needs truly protected is your steering column. Some even just wrap a black trash bag over the steering wheel and call it good. There is a clock spring I think it is in there that basically is hooked to everything from ignition to dash lights and headlights. That gets wet I think your SOL... You'll be surprised how often you start checking weather once you take your top off this spring. If you have a hardtop I would recommend keeping the freedom panels with you even when naked just so you have something to seal up over the front seats if a big shower comes. With a soft top it's not much hassle to throw it up every night when you park and just leave the rear windows out of it.
Yes, it is the clockspring that is the most expensive to fix (outside of electronics). Some people have been REALLY lucky, and their clocksprings have dried out after a rain and not had a problem. Others have had their dash light up like a Christmas tree. To me it's just not worth the risk.
Second thing to worry about is electronics. None of the jeep radios are water proof or even water resistant. If you add an aftermarket stereo, it's an even bigger replacement cost. You can find water resistant marine speakers, but I don't know of any marine stereos that people would run in their jeep.
If you're planning on leaving home completely topless, the RainGear cover is awesome. It fits tight. Works top on/off, doors on/off. I got one for Mike's jeep and we love it. You can't drive with it on, so if you got caught in a storm while driving, you'd have to pull over till it's done, but there aren't any emergency tops that are rated for over 45mph. Here in Texas where most roads are 70-80mph, an emergency top just wouldn't cut it.
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