Definitely add in a flex coupler to prevent the manifold from cracking, it really helps on the 97-99 4.0L engines.
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As far as exhaust, a larger Magnaflow muffler has a deep rumble without being too loud. The Thrush Hush muffler mentioned above is a turbo style muffler. Dynomax makes a "super turbo" catback kit for the TJ that will sound very similar. I had that kit on my XJ and it was nice and tame, a bit deeper than stock with a nice idle.
https://www.amazon.com/dp/B00104H2YC/?tag=wranglerorg-20