There are plenty after market exhaust systems that will fit your jeep.

What is better than stock?? Thats your opinion... I personally enjoy a quite car, but some people love a loud rumble. Either way, since you need the piping and muffler, you want to buy a "cat back exhaust system". This will come with the muffler and piping to get from the cat to the back of the car, including a new tail pipe.
cat back
I'm running a dynomax system in my jeep. It's cheep, quite, and fits well.

The new style exhaust manifold with expansion joints for number 1 and 6 cyl. supposedly fix the problem of the collector cracking from heat related expansion fatigue (I am currently running one).

These guys have 2 manifolds that would fit your jeep
manifold



In order to get the old bolts off, spray them down with PB Blaster, or whatever your favorite penetrating oil is, and let them sit for a few hours minimum. Use a 6 point socket on all the rusted bolts, a 12 point will probably just strip the sticky ones. You'll find that the bolts going into the head will be probably the easiest, the bolts on the collector and cat will be the hardest.