Replace the muffler. There is a delicate balance between the air and fuel going into the engine and the exhaust coming out and that is thrown off by that trashed muffler. Replace the muffler, reset the computer (pull the fuse for it and leave it out for a few minutes), then drive it like normal for a few days so the computer can get all it's readings and adjustments set right.
Now for a more technical explanation, just in case you understand this stuff and want to know why -
Right now your engine is running lean, it's starving for fuel and air. Why is that, you ask? Well, we'll take this from the exhaust stroke of the engine cycle. When the piston is traveling upwards to push out the burnt air/fuel, the exhaust valves open. As the exhaust valves start to close (but while they are still open) the intake valves open up to allow fresh air/fuel to enter the cylinder. That overlap is always there, and a little bit of fresh air/fuel will always slip out. No big deal really, it actually helps to keep everything cool in the engine.
The thing that prevents too much of the fresh air/fuel mix from escaping when the valves overlap is the exhaust backpressure. If your exhaust is too restrictive, it won't allow enough fresh air/fuel to exit and your exhaust valves will start cooking and your exhaust manifold will get too hot. If your exhaust is too loose, too much comes out during the overlap. You will start getting more carbon build up within the exhaust, clogging it up, and, oh, the most important part...there won't be enough air/fuel in the cylinder to make enough power. It will still run, enough will stay in there to keep the engine firing, but it's not a good situation.
Your jeep is a 98, so it's OBD-II equipped (that's the type of computer). It has more sensors than an OBD-I system (all cars from 1996 to the present have OBD-II systems), which help to maintain fuel economy, lower emmissions, and the computer takes constant readings of what the engine is doing and makes adjustments to keep everything running smooth.
You, however, are not running smooth right now.
The OBD-II system is more than likely sensing a "lean" condition in the engine right now due to that loose exhaust. It is trying it's best to compensate by having the injectors spray more fuel and have them spray longer, but unless you've changed your air intake, you are not capable of providing enough air for that fuel, and unless you've changed your injectors and reprogrammed the computer, you are not capable of providing enough fuel to compensate. The OBD-II is doing what it can with what it's got, but it just isn't enough.
If you get the muffler replaced, you will restore the proper balance to the intake/exhaust of the engine. I highly suggest resetting the computer so everything is cleared, that way it doesn't start off trying to dump too much fuel into the engine to compensate for the loose exhaust flow that it will still think is there until all the readings have been taken by the computer. It will go back to a default setting and begin taking it's readings and making adjustments where necessary.
It may take a few days, although it shouldn't, but we are talking about a Jeep here. See, with the older OBD-I systems, you could reset the computer and it would get back to "normal" faster. The OBD-II has to be "put through it's paces" with a variety of driving...city, highway, stop and go, steady speeds, accelerating from one speeed to another. It's complicated but it takes a lot of readings and makes a lot of adjustments. All you really have to do once you reset the computer is drive like normal and the OBD-II will eventually make all those readings and do all the adjustments.
If there are still problems after getting the muffler replaced, well, it's just like Harleys...you can't fix something that's incapable of being fixed.
Get the right muffler put on there, don't opt for a "higher flow" muffler, get an OEM or OEM replacement. It will provide you with the right amount of pressure to keep things running the way they should. I laugh my testicles off at the stupid ricer fags that put high flow exhausts on their shitbuckets. 99% of them have no clue how an engine works and they are running lean as hell, losing more power than they gain. Sure, they think they gained power in the higher RPMs, but it's only because they've lost so much in the low RPMs that when they do make power again, it feels like they're faster. Sorry ricer fags, it doesn't work that way, you lose, put a bullet in your head and don't try again. The engine is meant to have that delicate balance on both sides, if you made an adjustment on one side (high flow exhaust) you have to compensate on the other side (high flow intake and larger injectors).
If you have any more questions feel free to ask. I'll be popping on and off the computer all day. I've got a few new victims that I'm going to skin alive, but that doesn't mean that I'll be too busy to discuss this further. It's fun to listen to them scream while I'm in the other room goofing off.
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