I posted this over in the Cherokee section, but I don't know how much action it'll get there, so I thought I'd try here too-

I have a 98 TJ w/ 4.0 and am here all the time, but I am trying to figure out an issue with a friend's 93 Cherokee with a 4.0...Using an inductive timing light, it has an intermittent miss in # 2 cylinder only-even swapping an ignition wire makes no difference, it has the same intermittent miss in #2.. The wires, cap and rotor are new, as are the plugs...I think there must be some kind of issue with the ignition module, anyone have any ideas? Since we ruled out the wires we removed the cap and looked at it but it looks, well, new. He is still going to take the cap back to autozone to get another, just to see if that is the reason. There is no check engine light, by the way.

Ideas appreciated.

anyone?

Let us know after you get another cap and rotor. But that should not cause a intermittent miss. Run compression test and see what you get.

Could a partially clogged fuel injector cause intermittent miss fires? Just a guess...

Yes, but he, I assumed when checking with the Timing light would get no light. that means the voltage is not in the line, that or a cheap light.

It does not take long with a bad plug or wire or cap to foul the electronics up.
A carbon spot in the cap or wire will lead to all kinds of issues. The fact it does not move when swapping lines says its more likely the cap.

See if you can spin the cap around 180 degrees. Some will let you do this, some will not. That should put the cap in a different orientation.

A clogged fuel filter or bad compression will not give you an inttermitent spark. Your rignition system's function is to provide spark to the plugs, it has no idea what else is going on.
If your getting an intermitent spark, it could be a couple of things, if the plug is bad, it could be internally grounding itself out, and thus you will not get a spark, bad cap, coil going bad and then off to the computer that controlls the spark.

You said you tried moving the wire, did you guys try swapping the plug with a plug from another cylinder? It might also be worth swapping the number 2 injector with another cylinders as well. That will help eliminate them as problematic. I had been dealing with a cylinder 1 misfire on my TJ and these were steps I took when I was troubleshooting.

someone in the Cherokee forum suggested pulling that plug and I planned on getting over today, but my other half had other ideas (gardening, I am the laborer) so that didn't happen...but I think that makes the most sense, it wouldn't make any difference if the injectors worked or not, I get steady ignition in all other cylinders with my inductive timing light (not a cheap one), but in number two, it is sporadic at best.

I'm going to get over there tomorrow to pull/swap that plug, I also think the cap might be an issue, it is certainly easy enough to change if the plug swap doesn't pan out.