I've had the exhaust done on both of my TJs and each time was never charged more than $250. The third cat under the vehicle can be removed as it doesn't have any effect over check engine lights. That eliminates the cost of a new cat (which is expensive). From there all you're talking about is basic piping and a muffler. You can pay more money for a tip, but I always just have them use a piece of pipe for the tip and angle it slightly down. The last thing I want is an ugly chrome tip or something like that.
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@Jerry Bransford had his exhaust done for a similar price as well.
Those "bolt-on" kits might be using stainless steel piping (which ads to the cost) which is nice, but not necessary by any means. In addition, they are usually have chrome plated mufflers, nice tips etc. Nice, but a bit too nice for a TJ. Not to mention they're charging for the name and the fact that it's a "kit".