For a rig that age, if you're going to do the water pump you'll be almost halfway to the timing chain. It's a bigger job, but I'd do it. Not only is it good insurance against the old chain breaking and stranding you, but the wear on a timing chain degrades your engine's performance by sending the valvetrain slightly out of time. I've seen a new timing chain just breathe new life into a tired old engine.
Check your motor and transmission mounts. The rubber breaks and rots away, and then your drivetrain wastes energy flopping around which could be pushing you down the road.
If the engine's a 4.0, check that the exhaust manifold isn't cracked. The stock units had that problem a lot.
No one thinks about the PCV valve on these rigs. New ones are a little hard to find for some reason, but I'd replace it when you do the ignition tune up. Check all the vacuum lines for rot while your at it. The molded rubber ends on the plastic lines can look fine, but when you squeeze them you can tell they're weak. They like to rot out or develop cracks on the underside where you can't see them.
A few things to watch for on the fuel injection system...
The electrical connectors at the fuel injectors get worn, and then the injectors start missing intermittently. It has to get pretty constant before it triggers a trouble code in the computer. I had one on my 4.0 that was missing maybe one in 7-10 hits. That was enough to make the rig run a little off, but not enough to trigger a code. I've heard that you can pop the connector off and bend the contacts to make them engage better. I just replaced that connector altogether, and planned to do the rest. You can diagnose this problem with a mechanic's stethoscope. Put the probe on the injector and you can hear them ticking as they fire.
There's an air temperature sensor on the intake manifold. Jeep cheaped out on this part; it's just a bare thermister hanging down in the airstream in a little plastic cage. They can degrade in that hostile environment and cause vague drivability issues that are hard to trace. I pulled my old one out and it looked terrible; dirty and discolored. Put a new one in and the rig ran noticeably better.
The crank position sensor is notorious on these engines. When they fail the rig just quits cold and you're stranded. If I was making long trips in my yj, I'd carry a spare and the tools to replace it.
