Just putting this out there for anyone who might be in my situation:
i had a hell of a time figuring out a cylinder 3 misfire. 2001 cherokee with a 0630 head swap. Only 145k miles.
first i replaced injectors cause the liners were cracked.
new spark plugs.
new heat shield kit for injectors to solve any heak soak issues.
it continued to misfire, and a stethoscope on injector three told me it would stop firing after two/three minutes runtime, the same time the cleared out code would pop back up.

i wired in a new connector to the injector harness for cylinder 3, nothing. Also swapped around injectors like 4 times. Nothing.

i ran a compression test to rule out anything mechanical. The results were even more confusing:

EVERY cylinder was low on compression (~90psi) EXCEPT cylinder three, the one that kept misfiring (130psi on cylinder 3)
did a wet test, bumped all cylinders up to spec
(135-155psi) so rings were probably sticky or just old.

but at this point i noticed my cylinder three spark plug still looked brand new, like it came out the box. Every other plug was sooty. Super sus.

but EVERYTHING told me that the coil rail is a batchfire system, its not bad if its a single misfire, it fires two times, etc etc.

Before i decided to rip open wiring harness and swap around ecu’s, i figured i might as well just buy a coil rail and see if that did it. I honestly had no hope that it would.

sure as shiitake, slap on a new coil rail, fire it up, thing runs like a top! All other codes are gone too (o2 codes and evap stuff) so my CEL is gonzo.

just wanna throw this out there for anybody that has similar issues. Im all for diagnostics over throwing parts at stuff, but sometimes ya gotta go with your gut. Hope this helps, and thanks to anyone who’s helped me along the way. This thing has hurt my smooth brain the past couple weeks, but man if it didnt feel like christmas lugging that thing around yesterday.
best of luck yall!

Interesting, that would have stumped me too. I'm guessing one side of the coil secondary was shorted or arcing to the block somehow.

Yeah idk its pretty weird. I havent made brackets to mount the rail yet so its just hanging out.

Well at least this gives me a reason to put back on the coil bar and see if my P0301 still pops up.
Did the coil mod sometime ago and really hate to think the new Mopar JK coil I used is bad but.....
I kinda wondered about the coil but cause of the wasted spark thing thinking if it is the coil not having 2 cylinders misfiring meaning it wasn't didn't seem like a stretch.
Now to just find where I put the damn coil rail.
LOL.

yeah i’d get some cheap new copper plugs, slap it in and try to run it. If cylinder one’s plug looks like new, thats prolly the issue.
i think the ECU will cut fuel to the cylinder once it realizes its not sparking. Every startup for me the injector ran for like two minutes, immediately cutting out when the computer realized what was going on, like clockwork.

That being said tho i hear a cyl one misfire is one of those naughty naddies that wont go away. Best of luck man!

Been running nothing but Champion Copper Tops, 438's to be exact, for over 10 years now.
Already threw a new plug in there knowing that probably wouldn't solve it.
IMO misfire codes are really just the a symptom of a deeper problem.
Having said that sometime ago I had a P0304.
Simplest thing first. Threw in a new plug.
Sure enough.
LOL.

If you don't mind me asking you for some insight? I'm have the same issue only mine is with cylinder #2. My 2001 Cherokee ran well until Sunday. I did and oil change an radiator flush. When I flushed out the heater core (which I've done numerous times) one of the hoses slipped from the top side of the fender wall where I had lodged it so that the water would flow over the fender and on to the ground and wouldn't soak the engine. In doing so it sprayed water on the back of the alternator and on the coil rail near plugs #1 and #2. I've gotten that area wet before when cleaning the engine, so I wasn't really concerned. However, after I completed the projects, I cranked it up and got a P0302 code.

My symptoms: It cranks with no problem, the idol is a little rough but with no discernable RPM loss, but when you drive off you can feel that something is not right. If you accelerate after a full stop there is loss of power and if you drive up a hill you can really feel a roughness and loss of power, like you're down a cylinder or two.

Here is what I've done so far: I've removed the coil rail, and dried it really well with an air compressor, I've done an OHM test on the rail itself and the readings are consistent at 0.80 for each pin. I've replaced the rubber boots and springs on the coil and installed new plugs. I have also taken apart all know electrical connections around that area such at the connection to the camshaft position sensor and blown them out with air. BTW when I pulled the old plugs the insulator tips all had a normal white color to them, except for #2 which was a darker brown color. It’s my understating that coil rails rarely fail, however are there any tests I'm missing before heading over to the fuel side, as you did? If indeed it is the coil rail, what brand rail did you buy? I know they're available at all the major part stores, however I've also read that this is a part you might now want to chance to an aftermarket.

Thanks!