Don't worry about the sway bar, leaf spring vehicles don't really need them all that much. I, along with many other people, have removed the track bar and sway bars. Usually the YJ will ride better without them. They aren't necessary, just something to get the NHTSA to shut up mostly. On a vehicle with coil springs, yeah you should probably have them on, otherwise you're in for a fun time when you turn at intersections.
The clicking sound could be several things. It could be an exhaust leak at the manifold, which isn't hard to fix. It could also be valves which isn't cheap to fix depending on who's doing it. I've seen worn out and wobbly pulleys make clicking noises before, not on Jeeps but on other vehicles.
You'd have to stick your head in there and try to pinpoint the location for us to be able to tell you accurately. Then again somebody will probably come along who knows what the problem is with just that bit of information.
1991 YJ: Daily Driver
1992 YJ: Pile of crap sitting in the garage.