I've got a 99' V6 4WD 5spd 4Runner and it has an intermittent misfire in cylinder 4.

I replaced all the spark plugs and that didn't fix it
I swapped the plug wires where they plug into the coil packs and the misfire followed the swap (the code read for a cylinder 6 misfire)
So then I replaced all the plug wires and that didn't fix it
Then I replaced the coil pack and that hasn't fixed it

Here's what I don't understand. If it is the fuel injector, why would the misfire have followed with the wire swap?

When the engine has been sitting for a few hours and I start it up there is usually no misfire or choppy idle. When I start it up again after its been running for a bit the misfire and rough idle come back. If it is the cylinder or the fuel injector I can't figure out why the misfire would come and go.

Sitting for a few minutes after runtime can cause a run rough condition for a little, this is common and usually no big deal. Sounds like you need a fuel injector. If it's bad then it's bad, it won't change no matter what ignition parts you replace because it's a fuel delivery problem not a ignition issue.

hmmm, have you ever cleaned your MAF sensor?

p0304?

Did you try swapping it with a different coil pack? like 1 for 4 instead of 4 for 6.

Wait a sec. So where is the miss now? back at four? If I understand you right, you mis routed two of the three wires so you should have been missing on BOTH 4 and 6. I'm surprised it ran at all, but not surprised that only one code set right away. They take a while. The other would have set eventually. If you are still getting P0104 with new coil, new wire, new plug, than yeah, injector or compression are what's left.

When you did the plugs and wires did you also replace the plug boots on the coil pack side of the engine?

I battled with intermittent misfires for a while and finally eliminated them by replacing the boots under the coil pack.

the wire set I bought only had the boots on the driver side cylinders.

EDIT: Just realized that both 4 and 6 are driver side plugs.

So with clogged injector or compression issue is it possible that at times the engine will run fine and other times it misfires? Because if that's not possible, meaning the misfire does not come and go when it is the injector or cylinder that is at fault, then despite replacing the coil pack, plug wires, and plugs I would be concerned it is still electrical somewhere further upstream in the wiring.

I wasn't supposed to swap the wires at the packs huh? Instead I should have removed the whole packs and switched them? It ran like shit and I stopped when I heard arc-ing. It was only a couple minutes and long enough to pull codes. In the bank were cylinder 6 misfire, cylinder 4 misfire and random cylinder misfire so you are correct. That was never made clear to me when I was advised to swap the wires that doing so just where they plug into the coil packs is not the right idea.

Personally for me, first thing that comes the mind when there's a misfire that gets worse with heat, I think coil. Boot could be the culprit, but coils don't like heat. A bad boot will always be bad. If you are going to switch the coils, tare the whole coil off and disconnect all wires. Then move it to the other spot and plug in the connector and spark plug wire (for driver side) for the coil that is supposed to be in that position. The misfire codes will stay in memory until cleared with a reader.

Your thought process on heat impact on coils is is spot on but remember that there is a coil in each injector as well. The coil in my problem injector would work fine when cold and then go in and out when hot. It tested good when cold but then tested open after operations for a while....

Buckaroo

You can switch just the coil, or you can switch the wire at both ends, if you want to test the wire, or you can swap both together, as long as you maintain correct routing of 1-4,2-5, 3-6 (difference is always three.) What you should not do is anything that does not maintain the routing and that is what happens when you swap one end of the wire.

I don't think there is any rule that says intermittent misses are only spark, only fuel, or only compression, or never any of the above. That kind of assumption will bite you in the you-know-where. The miss detection system is slow and funky. We're lucky it works at all.

So to bring the mystery to a close... I pulled the fuel rails and tested the resistance on each injector. All read between 13-16 ohms. I flushed each injector and all the ones I pulled from the scrap yard using this method, which I found to be the simplest and most effective on YouTube. Each injector had a good clean spray pattern... perhaps Techron's fuel system cleaner really does work.

I took the cylinder 4 injector and two of the spares from the scrap yard and put them in a toaster oven until they were warm to the touch. Checked resistance again and the two spares read around 20 ohms and the cylinder 4 injector didn't read at all. Problem solved!

Great technique! Glad you got it figured out......

Buckaroo

Pretty cool and cheap method to clean injectors I saw a commenter mention direct 12v to the injector may damage it; a 9v battery should suffice, the low current output shouldn't harm anything.

OP good idea re-testing the injectors at "operating temperature"

It's a wonder Toyota doesn't have a way to monitor the injector circuit like American cars do. Unless they do and it didn't catch the injector coil opening. My jeep and Saturn have pull up resistors in the circuit and a monitoring circuit. If the circuit opens in any way the monitoring circuit goes high and you get a code. If wiring or coil shorts to ground the circuit goes low and you get the same code (injector X open or shorted code for jeep or a quad driver circuit failure in the Saturn)


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Amazing ingenuity