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Since it's a 98 it has a distributor ignition, (no coil packs) have you ever had it tuned up? Change the spark plugs, while they're out check the compression to eliminate a mechanical problem and replace the distributor cap, rotor and wires and it should be good to go.
The exhaust leak could be a cracked exhaust manifold which is common for 6cyl wranglers. But 130K miles is really nothing for that engine.
If replacing the ignition components (plugs, wires, distributor cap, rotor) doesn't fix the problem, then that injector may not be operating properly. Check the fuel injector and its associated plug and wiring for the #5 cylinder. It may be leaking, spraying a bad pattern or spraying at the wrong time.
The exhaust leak in the muffler will cause the backfiring and the CEL problem.
Okay...I think I will start with this as it's something that obviously needs to be replaced anyway. Could very well be the original muffler and it definately has about a one inch long leak along one of the seams.
If replacing the ignition components (plugs, wires, distributor cap, rotor) doesn't fix the problem, then that injector may not be operating properly. Check the fuel injector and its associated plug and wiring for the #5 cylinder. It may be leaking, spraying a bad pattern or spraying at the wrong time.
When I was earning a living with a wrench in my hand, we called this the "shotgun approach". Instead of isolating the problem and fixing it, just start shooting parts at it, hoping one of them will be the one that fixes the problem.
Yes, based on following advice from those who should know better, I did the same thing, even though I DID know better. But, finally, I did pay to get the definitive diagnostic done, and discovered the REAL problem.
I strongly recommend the same approach. Instead of throwing parts at it, find the real problem and fix it.
The misfire will likely activate your check engine light, and you won't pass a smog test with the light on in a state that requires smog testing. Its possible to deactivate the CEL with a scantool or pulling the battery cable as some try to do but that won't work either because the smog test machine will detect that and automatically fail you.
Get it fixed properly by a good smog technician. There are a 1000 things that can cause a misfire and trying to fix it yourself is a lost cause.
If replacing the ignition components (plugs, wires, distributor cap, rotor) doesn't fix the problem, then that injector may not be operating properly. Check the fuel injector and its associated plug and wiring for the #5 cylinder. It may be leaking, spraying a bad pattern or spraying at the wrong time.
An easy way to check the injector is to swap it with another one, say #5 for #1 and see if the misfire moves. Since the OP has knowledge that it's #5 he must have access to some sort of diagnostic tool.
One further comment- I am noticing it doesn't misfire when it's extremely hot and dry out.
Runs like a champ when it's above 105 out. I don't think I could even replicate the problem at or above that outdoor temp.
The engine obviously is running same temp as always according to the gauges so maybe something with double digit humidity (like 14-20 percent) is triggering the misfire?
Not sure if this points anywhere just hoping it may narrow things down a bit.
Plug in a scan tool and look for codes (active & stored). Could be as simple as bad plugs or coils.
Prolonged misfire can wreak havoc on catalytic converter$.
Right answer here. Switch the coil on the offending cylinder with another. Clear the code and if it misfire follows the coil, than its the coil.
Coils going bad can also be caused by oil leakage from the valve cover gasket which may be affecting the others soon. You would want to address that as soon as possible for that reason.
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