I have an N/A '98 Cobra with 4.30s. I too struggled for a while trying to figure out which gear to put it. After talking to many Cobra owners the general thought seemed to be, "These cars love to rev, so don't fear the gear." So I crossed my fingers, threw in the 4.30s, and have never looked back.
Funny story. My buddy has a 99 GT with 3.73s. I let him drive my Cobra to see what he thought of it with the 4.30s. He stomped on it in 2nd gear and shifted to third very shortly thereafter. I said to him, "Dude, what the hell are you doing?! You still had 1500 rpms to go!" He immediately responded, "Holy **** dude. 4.30s are perfect on a Cobra. You can still rev out each gear much longer than my GT, but it gets up into the power really fast!"
On the freeway in 5th gear at around 70mph I turn somewhere around 2700rpm -- that's about a 700rpm increase over the stock gears. At first it was a little nerve racking seeing the tach a bit higher than usual, but these motors are meant to rev. And besides, what the hell did you buy a Cobra for anyway? To cruise on the freeway? Hell no. You got it for acceleration, or at least I did. Also keep in mind that by lowering the gears, you might not lose any top end. A '98 Cobra probably can't hit redline in 5th gear stock, but by lowering the gears 5th ends up actually being usable (compared to an overdrive) and can more easily approach redline. I've never tested this, as I don't care about top speed, but it's an interesting thought.
By the way, I primairly drive my Cobra around town/cruising on the weekends -- maybe at the dragstrip once every few months. So you can kinda get an idea of how and where I actually use my gear. I use it mostly in the "real word," so to speak.