So first the important details. 2001 body and computer...1998 motor and exhaust, modified to install 2 -- o2 sensors...1 in each main pipe before the 2 into 1 collector. And 2 more sensors in the single exhaust after the secondary cat. I have never thrown a cat code or a sensor related code.Stroked to a 4.7 ish with a torquer cam. Coil rail eliminated using Screaming Demon HV coil pack . Wrangler 3.2 ..27lb injectors. 3 years since build. It has run excellent for 2 years but now i get a cel #2 cyl misfire fairly consistently ONLY at idle. New plugs...changed out injector..criscrossed the #2 and#5 coil pack spark plug wires . Sprayed around the manifold and injectors with starter fluid to check for a vacuum leak..didn't seem to find one. Number 2 compression is 152 and #3 is 160 psi. I didn't check the rest because it was similar to a year ago. I was expecting something radically off. All plugs removed were clean showing signs of running leanish but the motor never pings. Scanner shows bank 1-2-3 O2 sensor running quirky with a non normal sine wave between 1/2 and 1 volt.I unplugged the front O2 sensor to put ithe fuel system into standby mode..no help still feel the miss at idle. Perfectly normal at speed .only thing the scanner shows is that at idle my timing is fluctuating between 4 and 10...when not broken it was a steady 10 i know the timing is computer controlled but i can't find what actually drives it..thanks in advance

 

Ok did you check the injectors ?

 

I replaced the nbr 2 injector with a new one.. it feels like its firing like the others. Only issue i see with the scanner is ignition timing eratic , cycling between 10 or 11 and then dropping to 4 or 5 then back to 10. Im out in the woods so i cant do too much t/s. I changed the cam synchronizer sensor cause its easy. When i laid all the plugs on the table , if i mixed them up...you couldn't pick out nbr 2 from the rest. The compression is ballpark same as the rest so i assume that rules out lifter or valve issues . I got a mopar cps coming next week, if that doesn't do it i will change out nbr 2 and 4 injectors and see what happens. I only throw code at idle...i think i feel it ocasionally. It started getting worse within the month for no obvious reason from once ever 2 or 3 months to one a day give or take

 

So i replaced the cam sensor the other day...it "felt" smoother but #2 cyl misfire still popped up later in the day while idling. When i get home i will probably have my mopar crank sensor , the one in there now is probably 01 original. I cleaned those connectors the other day but no help.

 

I had similar problem on my 2000 xj and could not cure it. So I ordered the viper coil mod from https://www.ksuspensionfab.com/store...oil_Mod.html#/ , no more ignition problems.
it run smoother, idles great, much easier to start and troubleshoot. I don’t have a dog in the hunt just satisfied customer.
CH

 

My 99 had a short on the cam sensor lead where the lead insulation was worn through.
I really don't know how your 98 is wired but my cam sensor is in the distributor and the sensor
lead exits the side of the distributor and feeds into a harness connector. The short was in the
harness after the connector. I've also had to repair the injector harness. I found a couple of
bad injector connectors so I bought new connectors on amazon and replaced all six. Soldering iron
and heat shrink tubing (with adhesive makes it water-proof), good was new!

 

I have the coil mod...running screaming demon coil pack assy..made for 2007-2011 wranglers...something above 60,000v. I have already swapped the wires between #2 and#5 and it still faults #2. I am going to have to get some noid lights to see the injector pulses...my scanner cannot read them. I had not done any mtc prior to the issue. It was running excellent and then....snap ...#2 misfire only almost every day or two The cam sensor is slightly different on an 01 but serves the same purpose. There are only 3 wires to it so i can't see how any failure internal or with the wiring could only affect #2 cyl. I asked once how the computer determines misfire and i was told by the O2 sensors. Can't argue that but when i have truck off and no codes....if i disconnect the bank 1/1 O2 sensor and then start it up ...after 2 or 3 min i get a bank 1/1 O2 sensor fault and a nbr 2 misfire. That sensor reads output of cly 1-2-3 so why only nbr2 fault. Need more internal workings info

 

Ok something odd...still throwing only cyl 2 misfire code but every once in a while it disappears on startup when it was there the night before. I thought you had to erase codes with the scanner. What might it mean if the cel self clears on startup...thanks

 

This is a shot in the dark but you mite look at the valve springs and rocker arms .

 

Yes thats a plan for my days off later in the week...i would be surprised if that was the cause since my compression on #2 reads normal but worth a look

 

Did a ton of stuff today...had a buddy's snap on scanner...nbr 2 misfire counter.....continuous even if I didn't feel it sometimes. Verified #2 plug fires visually and constant. Verified #2 injector lites noid light as same as nbr 1-2-4...made a jumper to parallel the light with injector so i could monitor while running. Appears crank sensor readings very erattic...waiting for new one tomorrow. Found cam syncro off reading -19... readjusted to 0 +/- 1.... no help.. inspected cyl 2-3-4-5 with boroscope...3-4-5 all aluminum looking...nbr2 was brown. Performed compression check...1-3-4-5-6 all 160-165 nbr 2 was 155-160.. tested nbr 2 several times. All similar .running a 4.8 stroker with a hi torque cam. All spark plugs look identical Pulled off valve cover and ran engine...all rockers and pushrods seem to operate the same will upload a hundred photos tomorrow. If its not the crank sensor im at a loss

 

Can you look at the injector waveform with that scanner?

Should look like this::

 

I might be able to but i think i have to disconnect the injector to do it, it has an oscilliscope function. Is your photo with the injector connected or disconnected

 

It is connected. I use push pins to make contact in the connector.

Monitor current, voltage and the point when the injector closes. Get a baseline from the known good ones.

 

Push pins: