3.4L misfire after intake repair

My wife's '99 Alero (3.4L V6) developed the famous intake coolant leak, so I pulled the intake and installed new gaskets (the new metal design). Now it has a BAD misfire that causes the SES to blink. It
started as cylinder #3 (P0303), so I moved that injector to cylinder #4, drove back to AutoZone and it was indicating that cylinder #6 now had a misfire (P0306). There were no problems (other than the water leak) before I "fixed" the car. I'm wondering if it is actually a random misfire, since there is no reason it should have changed from cyl#3 to cyl#6. When driving, it feels like it is a single cylinder, because there is a constant vibration from the missing cylinder that changes frequency with RPM.
Plug wires are on correct, I think it is either a fuel or vaccum leak issue. The fuel rail was leaking from the feed line when I took it apart, so I used some fuelproof sealant for threaded fittings. Now I'm wondering if I got some of that into the injector(s).
Any tips? I'm at a loss, wondering what to try next. The pushrods were kept in order & re-installed & torqued to spec. How easy would it be for a decent shop to troubleshoot this with a Tech-2 or more capable scanner, and how would I find such a shop?
Thanks for any tips!
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Check for vacuum leaks, maybe you missed a line when you put the manifold back on.
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SteveR wrote:

I'd be checking for some sort of vacuum leak. Did you lubricate the fuel injector o-rings before you re-installed the rail back into the manifold? I've seen these o-rings get pushed off if they aren't lubricated in some way. What about the upper plenum? Did you make sure the surfaces were cleaned up....no old gasket left on there?
In this case, the tech2 will probably do nothing more then indicate which cylinder is missing....other then that, it's just try to figure out what you missed.
Ian
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In article

Cylinders 3 and 6 share the same coil pack. Pull both plug wires off of the 3/6 coil pack, start the engine and see if the spark can jump between the two coil terminals. Check the spark plugs, maybe some coolant or such made it's way past an open intake valve.

I'm trying to picture what threaded fittings you took apart?? Two quick connects is all that is usually needed. Here is where I differ from Ian, I do not pull the fuel rail, I disconnect the quick connects and leave the rail and injectors in place. The 4 center lower manifold bolts -can- be accessed without rail removal. Installed in the manifold, the injectors are better protected. I cap the lines to avoid the fuel rail going dry, adding to the multitude of injector problems that these engines suffer.

Make certain that you don't also have a leaking fuel pressure regulator. And when you say that the pushrods were torqued to spec, tell us exactly how you did that.
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Nope. The fuel delivery is a threaded connection to the fuel rail. It has an O-Ring that seats inside the rail. The other line is the quick disconnect you're thinking of and is also O-Ring sealed, and it clamps to the rail. The OP should definately replaced the O-Ring and not tryed to cob a repair, but I'm not sure that is really the source of his problem. It's bad maintenance, but it may not be what's acting up now.

That's not a bad approach. I pull the rails, but it's just so I can get a look at, and clean the injectors. If the motor has +- 100,000 on it, it's common to find some crud in the injectors and a little carb cleaner does wonders to clean them up.

If he did it like I do, he gave them "one more tug".
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Thanks for the input so far, I appreciate it.
As for the fuel feed O-ring, I did replace the O-ring as soon as I realized there should be one there. It wasn't there when I took it apart so I didn't know it needed one. The fitting had been leaking, which is why I used the thread sealer. As soon as I realized the groove in the feed line was for an O-ring, I put one on there and of course the leak was gone.
When I said I torqued the pushrods to spec, I meant "per the book spec", which I think is 163in/lbs then 30 degrees. I even drew a 30* triangle and put it under my torque wrench so I could be as near 30* as possible.
Back to the originial problem...
I did lube both the injector holes & O-rings before I re-installed the injectors, and all of the O-rings are new. No gasket material was left anywhere on any surface, upper or lower. I'm really anal about that stuff, I probably spent two hours or more cleaning.
I did some more work on it last night, I don't think it is a clogged injector anymore. It continues to reset the P0306 (cyl 6 misfire) code after I clear it, enough that I am confident that it is that cylinder. I pulled the #6 plug, it looked awful. All the other plugs were just slightly white but normal, #6 had black crud caked on the electrode, and the center (platinum) electrode was cooked away (there was a hole in the porcelin where the electrode should be), and the plug was slightly wet, hard to tell if it was fuel, oil, or coolant though. Definately a bad plug, but unfortunately not the cause of my problem, probably just a symptom. I swapped that plug with #1 I'll replace them all next time I work on it, I couldn't get plugs at 11PM last night. I cleared the code and restarted the car, but it still gave me a cyl 6 misfire blinking SES, and no other codes. I was hoping it would travel to #1. So now I am really sure there is some problem with cyl 6.
I can hear a vaccum leak around the #6 intake "tube". Haven't been able to pinpoint it though, and I'm wondering if I'm really just hearing the IAC sucking air since the throttle is right next to #6. It is really pronounced when you kill the engine (sucking sound gets louder). I tried tracking it down using a piece of hose to my ear, but haven't been able to find it. I'm wondering if the lower intake didn't seal against the head.
I'm also going to try swapping the 3/6 coil with one of the other coils to see if the problem moves.
Any new troubleshooting tips? I'm sure the thick black crud on the #6 plug indicates something, but I don't know what.
Thanks again for the help and any suggestions.
Steve Ruse
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SteveR wrote:

Hmmmm, thick black crud typically means oil fouling.
I would do a compression test on the #6 cylinder next. Nothing you did should affect compression, but it would be good to rule out and is easy to do.
John
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Good idea, but he also said the electrode is missing, which sounds like detonation or pre-ignition.
Steve
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I meant the small, platinum, center electrode is cooked away, not the larger electrode. I'm sure you've seen platinum plugs, the electode in the porcelin is tiny, maybe the same diameter as a small needle. There is just a hole there now. I don't think it is detonation, I think that the platinum coating eroded away, and the rest of the electode easily eroded away. At least I've read that it can happen.
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Alright, sounds like you've got it under control....
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Here's an article to read: http://www.streetrodstuff.com/Articles/Engine/Detonation/index.php
Just to hear it from another source, when looking at the coils, posts up, the order is 1-4-6-3-2-5.
Not sure if you've done this, but start by checking all vacuum hoses and connections, plug wires, engine and PCM grounds and EGR to intake connections. Then look at fuel pressure, fuel injector operation and use a spark tester to check for proper spark at that cylinder. Maybe the injector connector got damaged during the repair? At that point I would personally take it into a shop for diagnosis, it's expensive but they'll usually quickly find the problem.
Here's the P0300 information if you would like it: http://users.eastlink.ca/~smackie/p0300.pdf
Steve
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A new O-Ring would have only cost $5.00 and would have been a *far* better approach to that problem. The only way to tell if you got any into the injectors now is to take the rails off again. Fortunately, that's not so much work and the gaskets for the upper manifold can be reused. Don't be cheap - go buy the damned O-Ring. You'll be glad you did. I've usually found some crud in the injectors when I pull them out. Did you? Grab a can of carb cleaner and clean them out good before you put them back in. Make sure you clean all of the sand and grit and dirt and crap out of the lower manifold ports for the injectors. Put a smear of vasoline around each of the injector O-Rings before reseating the rails.

I'd fix the fuel problem the right way before I took it anywhere.
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Anyone know what the final fix was for this repair.
Warren
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