Cannot fix Single cylinder misfire under load.

Brace yourselves! This is gonna be a long one!

I’ve been trying to fix a misfire for over a year now to no avail. I will post everything I’ve done to date and see if anyone has any suggestions.

I get no codes at anytime except the cylinder 3 misfire code that throws the truck into limp mode. All readiness tests complete within a day or so after resetting the CEL.

2016 Toyota Tacoma TRD Off Road 3.5L V6 6 spd auto

Feb 2022
165k miles
Just outside of Dallas coming home from Mississippi the truck had an intermittent, but noticeable miss.
Miss became worse and would put the truck in limp mode with flashing CEL. Turn it off and back on again was the only way to drive around. I bought a
Cheap scan tool and it said cylinder 5 misfire.
I changed the plugs but miss was still there.
I swapped coils from 3 to 5 but miss stayed on 5.
I took it to a shop for diagnosis.
They determined it needed a high pressure fuel pump and an O2 sensor.
I replaced the pump with an OEM unit (Denso) but that did not fix the issue.
I took the truck to Toyota dealer for diagnosis.
They had it for 3 weeks driving it daily and could not replicate the issue, so I was told to pick it up.
I didn’t get a mile away from the dealer before it went into limp mode again.
Took it back to dealer and they told me the following day that a wire had broken on number 5 coil and that the coil needed to be replaced and the wire fixed. I approved the job.
Picked up the truck and headed home to Waxahachie (45 miles from Sport City Toyota). I was about 5 minutes away from home when I tried to accelerate around a car on the highway and the truck went into limp mode again.
Called the dealer and they sent a tow truck.
Got a call back a few days later saying they could not find any issue and could not replicate the problem.
I went to the dealer and picked the truck up, again not making it a mile before going into limp mode.
Went back to the dealer and this time the service manager drove the truck with me. I told him to step on it like getting on the highway and sure enough it went into limp mode.
We got back to the dealer and the service manager told me he was going to put his lead tech on it and we went out to talk to him.
The techs first question for me was “are you aware of the valve problems these trucks are having?”
I was not aware and he informed me that some of the tacomas 3.5l passenger heads had bad valve guides that wear prematurely and cause burnt valves.
He said he would do a leak down and report back.
Got a call from the dealer stating that cylinder 3 had a leak of 25% through the exhaust valves (not 5).
Was quoted $11k to do a new head, 2 exhaust valves on 3, both passenger side cats, direct injectors and O2 sensors.
I am a vintage motorcycle mechanic and felt comfortable doing the mechanical work since I now had an idea of what the problem was. I’m just not up to speed on computer controlled systems.
At this point I could not afford to do the work and still had to drive the truck to and from Dallas daily and racked up another 20k on the motor over a years time.
At this point, I was getting P0430 and P0420 codes.
The truck would drive fine with no misfires as long as I was easy on it and didn’t try to rev it too high.

Jan 2023
185k miles
I pulled the engine and tore it down.
Took the heads to a machine shop in Dallas, Cylinder Heads International.
Told them what the dealer had said about bad guides and said to replace all of them.
Got a call the following day from the machine shop and they said there was no issue with any of the valves or guides outside of what would be expected on an engine with 185k miles. They said there was no play in the guides.
Since I was already this far into it, I told them to go ahead and do a valve job.
While I was waiting on that, I pulled the rotating assembly out and checked all the bearings and bores.
Bores are
1 - 3.7035 -.0200 94.068
2 - 3.7025 -.0210 94.043
3 - 3.7035 -.0200 94.068
4 - 3.7035 -.0200 94.068
5 - 3.7040 -.0205 94.056
6 - 3.7035 -.0200 94.068
Standard from the factory is 94.000-94.012.
Maximum is 94.200.
Since the bores appeared to be within spec, I put in a new set of rings after a light hone to deglaze.
I also checked all rod, main and thrust bearings and replaced them all.
All torque to yield bolts were replace.
All gaskets and seals were replaced.
April 2023
Engine was reassembled and installed along with new denso O2 sensors and a set of used front cats from a wrecked truck with 23k miles.
Started easily but had a miss.
Scan tool says cylinder 3 and 4.
Installed new plugs. No change.
Swapped coils. No change.
Installed rebuilt set of direct injectors.
That solved most of miss, but it was still there intermittently.
Drove it for 2 days with no issues.
Third day as I was passing a car on the highway it went into limp mode again.
Cylinder 3 misfire is the only code.
At this point I am shooting in the dark.
I replaced all port injectors with a new set.
Still getting the same cylinder 3 misfire and limp mode.
Again the truck will drive ok (but weak) as long as I don’t give it too much load. Medium throttle at 3k is enough to throw it into limp mode.
I took it to another shop for diagnosis and they could not find any issues.
They noted that they can see misfires, but cannot find a cause.
Misfires can be felt at idle.
I started questioning the fuel pump/filter at this point.
Hooked up a pressure gauge at the port rail and read 50-60 psi which is within spec.I cannot check direct injector rail pressure without a high end scan tool.
While trying to find anything I could online about why this would happen, I came across a thread talking about others who were having similar high rpm misfire symptoms.
Reading into it, they all experienced a broken door/flap inside the upper intake plenum called the ACIS.
Apparently the shaft would break and the door would fall down and partially cover one of the passenger side runners.
I remembered that I heard a rattle when installing the plenum the week prior and I went and checked mine and sure enough it was broken.
My thought was that this flap had been the issue from the start and that it had lodged above number 5 previously. And perhaps I had shifted it to 3 when I had everything apart.
At this point I thought I had found the issue.
Ordered a used plenum with a good door and installed it.
Better low end, but truck still goes into limp mode with a number 3 misfire.
In the thread, many of the other people ended up having to replace plugs or coils supposedly from overheating from the misfires.
I swapped coils and plugs to other cylinders with no change.
I replaced the MAF just in case but live data stayed the same.
I did a compression test on the bank 1 cylinders. All read 150 psi. I then did a leak down to assure myself that the heads were done correctly and they all showed about a 1-3 psi leak, which I’m assuming is fine.
I contacted one of those online mechanics and chatted with him about everything that I’ve done and he seems to think it may be ECM related.
He thinks that the number 3 direct injector may not be firing during those medium to high load moments causing a lean misfire. I bought a used ecm, installed it and did the “handshake. No changes. Engine still misfires under load and goes into limp mode.
I can run the truck in live data and see that bank 1 goes lean under load (O2 sensor reads .100 - .250 volts while bank 2 reads .750 .800)
I can also see that when I floor it, both banks go rich so that leads me to believe that the fuel system is capable of doing its job.
I am curious if the rear Catalytic converters are plugged and that it’s causing too much back pressure? I’m out town for the next few weeks, but I plan on testing that when I get home.

If anyone can point me in a direction that my price fruitful, I’d appreciate it!

Are you getting misfires for only cyl. #3 still?

You need to have an oscilloscope hooked up while driving so you can see the spark and fuel controls while misfiring. The easiest way is to hook up a current clamp to the fuse that powers the ignition coils, and again for the fuse that powers the injectors. Compare signals between cylinders. SD has many videos showing this.

The fact that Toyota always said they couldn't replicate the problem sounds like they didn't want to tackle it and wanted you to go somewhere else.

have you tried a cam crank variation relearn? checked reluctors on cam shaft for play in and out or vvt solenoids for issues ohm test when issue happens. since its a under load issue could be a solenoid issue or coil or injector issue or just needs a relearn done.

JoshuaK wrote:

Are you getting misfires for only cyl. #3 still?

You need to have an oscilloscope hooked up while driving so you can see the spark and fuel controls while misfiring. The easiest way is to hook up a current clamp to the fuse that powers the ignition coils, and again for the fuse that powers the injectors. Compare signals between cylinders. SD has many videos showing this.

The fact that Toyota always said they couldn't replicate the problem sounds like they didn't want to tackle it and wanted you to go somewhere else.

I did just buy a picoscope 2304a along with some backprobes, but no amp clamp. I guess I should order one to do more testing. I am not familiar with what to look for unfortunately. I used it to look at cylinder 3 port and direct injectors. I was hoping to see something definitive proving the ecm was bad, but like I said, I’m not sure what I’m looking at and since the truck has port and direct injection, I’m also not sure which one is active at any given time.

I originally just tested the port injector on 3 and hooked the positive lead of the scope to the trigger wire on the injector and the negative lead to the negative terminal on the battery and I got a nice clear signal. I tried that exact same test the other day and hooked it up the same way and the ecm shut down the injectors on 4 and 6. I forget exactly which code they were but it was definitely for those two. I had to disconnect the negative test lead from the battery and then reset the CEL for the motor to run right again. I’m not sure why that was unless the picoscope test cable I’m using is faulty.

Hardtopdr2 wrote:

have you tried a cam crank variation relearn? checked reluctors on cam shaft for play in and out or vvt solenoids for issues ohm test when issue happens. since its a under load issue could be a solenoid issue or coil or injector issue or just needs a relearn done.

Unfortunately I do not know how to do that and I’m assuming I need a high end scan tool to do a relearn? How would I go about checking play? Pull the valve covers? I have assumed so far that all of that was good since there are two cam sensors per bank and a crank sensor. I assumed that the ecm would throw a code if they weren’t in sync, but I am not familiar with this modern of an engine.
Would a vvt solenoid go bad wothought throwing a code? I guess I could swap them (2 per bank) around and see if the misfire swaps cylinders?

A VVT solenoid shouldn't cause a single-cylinder misfire. One thing you could try is unplug the port injector #3 (the computer may use the direct injection only knowing that there's a problem with the port injector), and then do this test again unplugging the direct injector only. If this is happening under load and when hot, it would be the direct injector that the vehicle would be using. The port injector is for low load and while the engine is cold, as far as I know.

JoshuaK wrote:

A VVT solenoid shouldn't cause a single-cylinder misfire. One thing you could try is unplug the port injector #3 (the computer may use the direct injection only knowing that there's a problem with the port injector), and then do this test again unplugging the direct injector only. If this is happening under load and when hot, it would be the direct injector that the vehicle would be using. The port injector is for low load and while the engine is cold, as far as I know.

I’ll give that a try when I get back to Texas.

well there are a million different avenues you can go with on this...that are pretty simple, now that everything has been replaced and you still have the issue, are you sure you got all your connectors put together in the right spot?

If the wire for number 5 cylinder was damaged have you verified that number 3 is not damaged somewhere?

you can check resistance on the injectors,but for the sake of being complete I would be checking every single injector at this point....

The only thing you have not replaced is the harness so you have some really simple checks to make sure everything is adequate there.

STIMECE wrote:

well there are a million different avenues you can go with on this...that are pretty simple, now that everything has been replaced and you still have the issue, are you sure you got all your connectors put together in the right spot?

If the wire for number 5 cylinder was damaged have you verified that number 3 is not damaged somewhere?

you can check resistance on the injectors,but for the sake of being complete I would be checking every single injector at this point....

The only thing you have not replaced is the harness so you have some really simple checks to make sure everything is adequate there.

I could be wrong, but I’m 99.9 percent sure all the connectors are in the correct place and tight. I’ve put 5000 miles on it since putting it back together and it runs good until it doesn’t. I guess I need to start with the picoscope and see if I can tell what is happening, whether it’s a no fuel issue or a no spark issue. That bank definitely goes lean under load so I’m assuming it’s a no fuel
Issues causing the misfire.

A no-fuel misfire will create fuel trims that are more positive than a no-spark misfire. But both will create a lean condition = positive fuel trims. If you're under +10%, I would suspect a no-spark misfire.

JoshuaK wrote:

A no-fuel misfire will create fuel trims that are more positive than a no-spark misfire. But both will create a lean condition = positive fuel trims. If you're under +10%, I would suspect a no-spark misfire.

When I look at freeze frame data from the number 3 misfire, I’m seeing bank 1 stft at 3.9 and ltft at 9.4 while bank 2 is at -0.8 on short term and 2.3 on long term.
Oxygen sensor b1s2 was at .140 V while b2s2 was at .735 V.
B1s1 was at 3.131v and b2s1 was at 3.229.
Under load like when going up a medium grade hill, both banks go lean when reading sensor 2s, but bank 2 will richer up while bank 1 stays lean according to the sensor. If you push it too much under this condition, that is when the hard misfire will happen.

It's looking like you have a no-spark misfire, because if it were no-fuel, the fuel trims on Bank 1 would likely be more positive than they are.

What are your fuel trims during a heavy misfire?

What you should do is unplug the 2 fuel injectors for cyl #3 and go for a test drive and see what the fuel trims are while going up a hill, and compare that to what they are when everything is plugged in (if the same, it would suggest a no-fuel misfire, and like I said before, I think the direct injector is what would be used under load like this). Next, you can disconnect the connector for #3 ignition coil, and see what the fuel trims are. This should give you direction.

You'll probably need to hook up a scope to your ignition and fuel injector controls and use long wires so you can see it while replicating the fault condition. See if either are cutting out.

If you don't have a high end scan tool you should be able to take it to a shop that does and have them do it for you. And it won't cost a ton of money either. Checking play would involve removing valve cover and inspecting the reluctor (the thing that passes by the cam sensor) for damage to the notchs. (Ie bent away from sensor)as well as metal debris on sensor If none found then check if reluctor is loose but gently pushing and pulling on reluctor to see if it moves a bit. If sensor is mounted on front of timing cover versus top of valve cover check end play of the camshaft by pushing camshaft to back of cylinder head and the pulling it to front of cylinder head measuring the difference. This would be camshaft walk however this would effect multiple cylinders if this was the case. The only other possible thing I can think of besides injectors is rocker arms failing

JoshuaK wrote:

It's looking like you have a no-spark misfire, because if it were no-fuel, the fuel trims on Bank 1 would likely be more positive than they are.

What are your fuel trims during a heavy misfire?

I appreciate you pointing that out. Like I mentioned, I’m not familiar with what to look for with this type of system. Is there any way to see secondary ignition with backprobes, or do I need to get an amp clamp? I’m using a picoscope 2204a.

JoshuaK wrote:

What you should do is unplug the 2 fuel injectors for cyl #3 and go for a test drive and see what the fuel trims are while going up a hill, and compare that to what they are when everything is plugged in (if the same, it would suggest a no-fuel misfire, and like I said before, I think the direct injector is what would be used under load like this). Next, you can disconnect the connector for #3 ignition coil, and see what the fuel trims are. This should give you direction.

You'll probably need to hook up a scope to your ignition and fuel injector controls and use long wires so you can see it while replicating the fault condition. See if either are cutting out.

I’m not sure I can do that without de-pinning the connectors. Direct injectors are under the intake and each bank has one plug into the main harness. Port are easier to get to but still just the single plug per bank for the injectors. Coil pack is fairly easy to get to.
How would I go about testing with a scope?

You may have to de-pin wires at the PCM/ECM or any connector along the way that you can access.

As for spark: Since you've swapped/replaced coils and spark plugs, you shouldn't be concerned with secondary ignition, but rather ignition control coming from the ECM/PCM. You can test both control as well as current to see if the primary side is working. Current is tested via a current clamp, and often the best way is to install a fuse buddy at the fuse that powers the ignition coils (and you can do the same for fuel injectors), and use your current clamp on that wire that goes between the 2 terminals on the fuse.

JoshuaK wrote:

You may have to de-pin wires at the PCM/ECM or any connector along the way that you can access.

As for spark: Since you've swapped/replaced coils and spark plugs, you shouldn't be concerned with secondary ignition, but rather ignition control coming from the ECM/PCM. You can test both control as well as current to see if the primary side is working. Current is tested via a current clamp, and often the best way is to install a fuse buddy at the fuse that powers the ignition coils (and you can do the same for fuel injectors), and use your current clamp on that wire that goes between the 2 terminals on the fuse.

Ok, I’ll have to order an amp clamp.

Can I also measure resistance in the trigger wires from the ecm to the coil? It’s an intermittent problem, so if the wires are the issue, im guessing I’d see a slightly higher resistance than the other trigger wires?

Do you have a 3- or 4-wire coil? If so, the trigger wire is very low current -- it's just a 4-5v signal firing a transistor in the coil, so resistance isn't going cause this kind of a fault.

FYI: My Hantek current clamp is a copy of the Pico and it works well, for $60-80.

JoshuaK wrote:

Do you have a 3- or 4-wire coil? If so, the trigger wire is very low current -- it's just a 4-5v signal firing a transistor in the coil, so resistance isn't going cause this kind of a fault.

FYI: My Hantek current clamp is a copy of the Pico and it works well, for $60-80.

I’m making assumptions honestly. If I have an intermittent issue with a misfire with only one cylinder and I’ve tested the coils, plugs, ecm, valves and compression, then I’m looking at a wiring issue right?
That why I asked about testing resistance. I figured I’d see a difference between that cylinders trigger wire vs the others.
To be realistic, I’m not sure what to actually test. I don’t mind ordering another tool if need be, I just haven’t had a chance. My wife’s parents died last year and we just got back from their estate where we had to clean it up and have a sale. Luckily that went well and we’re now back at home where I can concentrate on fixing this thing. But again, I just don’t know where to look. I’ll order the hantek clamp today, I just want to make sure the connection is correct.
Btw, it’s a 4 wire cop