Weird Civic misfire problem
 

I have a 99 Civic EX (d16y8) with 170k miles and over the last several months it has developed a bit of a misfire. It's not really noticeable on the highway, but when under light load at about 2k rpm and at idle, it is pronounced.

Anyway, I've been trying to diagnose and hunt down this thing since it started. I recently got a timing light for christmas, so I decided to check my timing and noticed something interesting, whenever the car misfires, the light fails to pulse for that cycle. I presume this means that it is just not firing.

It's completely intermittent, and does not occur at regular intervals that would lead me to believe some rotating sensor was damaged, and it jumps across all 4 cylinders.

Just for posterity and in vain hope, I did a whole tune-up (plugs, wires, cap, rotor). Nothing changed. I checked the coil, which had the blue mark indicating that the insulation had been burned through, so replaced that. No change. Read an article about how ICMs sometimes go bad in older Civics, so I replaced that with no change.

The other day I pulled the whole distributor off to inspect for damage on any of the internals, but everything looked like brand new. Not even any dust inside it. All the magnets on the sensors were clean and free of metal flakes or debris of any kind.

Unfortunately, I can find no information about this kind of problem and no test procedures for anything that's left. Has anyone else ever encountered this sort of thing with their car? Seems like usually misfires come down to air and fuel issues and not spark, so I'm totally at a loss here. The engine light never comes on, and when hooked up to a scan tool for live data, everything reads right where it should.

I've seen the harness under the intake manifold cause weird issues on those year cars. Inspect the wiring found in THIS TSB

Also, your model civic has the crank position sensor located behind the Crank Pulley...inspect the wiring of that sensor to make sure it's not damaged.

Good call on the crank sensor wiring. I will check that out on my next day off. Is there anything specific I should be looking for there?

I actually saw that TSB not long ago when I had that load detector MIL go off and kill my car on the highway.I pulled out that harness and taped it all up when that happened, so I doubt that is the issue.

I know you said you've changed the plugs and plug wires, but I'd suggest checking both again. Check the plugs for the correct gap and cracked insulators. I've also heard more than once of people getting a bad set of wires, also check to make sure you got all the plug wires snapped into place good at the distributor and on the plug. Try starting the car in a dark area with the hood up to see if you see any fire arching from the plug wires. Have you tried putting a fuel drier in the tank to remove any moisture that may have got in the system?

I actually checked the gap on Sunday on the hope that maybe something happened to change it from when I installed them, but they're all between 1.0 and 1.1 mm, which is where the sticker says they should be. Visually, they all look pretty new.

I've tried spraying water on the wires to see about bad insulation, but haven't noticed any sparks. I had a couple of extra wires around the garage from another civic and have tried each set, but I get the same results either way. I checked the resistance on them, too, which isn't always 100% check, but they all came out at spec.

I haven't tried a fuel drier, but because of the way the timing light fails to light up sometimes, I'm pretty sure it's something going on in the ignition system (sensor or hard parts) and not an air or fuel issue. I'm not sure the car really sits long enough to acquire moisture anyway, since I drive it for like 3 hours a day and several hundred miles a week.

I like the train of thought, though.

I feel like I shouldn't be looking for unicorns on hearing hoofprints, but I checked all the places that horses live :).

is it always the same cyl or does it bouce around ???

Just an off the wall thought, have you tried the timing light on another vehicle. You said it is new, but if it is flakey it could be sending you off in the wrong direction.

I have tried it on other vehicles and it works great.

This misfire doesn't really bounce, so much as all of the cylinders are doing it at random intervals, though it appears that 2 and 4 are doing it *slightly* more, but I can't give a quantifiable number, there.