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Discussion Starter #1
Hi all, 04 LX 5 SPD 203k

I put new spark plugs, oil pan, valve cover gasket and a new oil pan gasket, 4 to 1 headers and 3 in exhaust. Cleaned the EGR also.The car ran fine during idle before replacing the header and exhaust. I painted the header and exhaust and started it up today to bake the paint. I noticed the engine running a bit rough. I pulled out my code reader and it shows no codes but, I checked the stored codes and it shows P0300, P0303 and P0304, yet, no check engine light. I had to jump the car because it has been sitting for a bit due to replacing the exhaust and headers. So, no check engine light, engine running a bit rough during idle and stored codes.
Any idea what might be going on? Would the new header and exhaust cause the engine to run rough?
The car ran fine before removing the header and exhaust.
I let it idle for about 20 minutes and roughness was still present. I figured since it sat for a bit maybe it's just the gas but, after 20 minutes it would have dissipated.
Could it be a weak battery? Again, I let it idle for about 20 minutes so the battery can charge.
The car ran fine with the new plugs prior to replacing the headers and exhaust. The first thing I replaced was the VCG, then the plugs. Started the car several times to verify any leaks and/or misfires due to the new plugs. Car ran great. Then I replaced the cam seal next to the EGR. Then cleaned the EGR and added a gasket since the PO removed the EGR gasket. Changed the oil and oil filter twice. Started the car several times. No issues. Then replaced the oil pan and oil pan gasket, along with the header and exhaust. I added a 90 degree elbow for the downstream O2 since it's an after market header with no cat. I checked under the car to see if there might be air seeping through the new oil pan gasket but, no oil leaks.
Does the ECU need to be reprogrammed because of the additional exhaust flow? The car was on E so I added about a gallon of gas. I completed the exhaust install yesterday and started the car and let it run about ten minutes. It ran great but, had to turn it off because I was performing the baking process and couldn't turn it back on because the battery wasn't strong enough to restart the car so I waited until today to start the car to finish the baking process. Started up fine then after about 5 minutes I noticed the idle bogging a bit. Checked for a CEL, no CEL. I decided to check for codes anyway and it said no codes. Then I decided to check stored codes and then I saw the P0300, 303 and 404 codes. Turned off the car, went inside to research what the codes meant. Came back out, started the car and the CEL came on.
Check the codes again and the same three codes are present.
I have not replaced the coil packs yet but, I doubt the coil packs would fail on cylinders 3 and 4 and P0300 means random misfires in general. P0303 and P0304 are cylinders 3 and 4. No codes on cylinder 1 and 2, just 3 and 4.

Thanks in advance..
 

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Discussion Starter #2
I researched the spark plugs and I thik I bought NGKs. The thing is, It ran fine prior to replacing the oil pan, header and exhaust. The first thing I replaced was the VCG and spark plugs. Restarted the car many times with no issues, which is why I don't think it's the plugs. I haven't replaced the coils yet but, I will swap coil one with coil four and see if the issue occurs on cyl 1. First I have to jump the car again. Can I swap the coils while the car is running? Don't want to risk damaging anything.
 

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I swapped coil 1 and 4 (car was not running LOL) and coil 3 and 2. Started up the car and no codes. The battery wasn't completely dead in order to wipe the codes. Let it idle for about 10 minutes, then got the P0304 code only. Let the car continue to idle for another 5 minutes and no codes (P0304 disappeared). Then 3 minutes later, a P0304 but, no CEL. I turned off the car and swapped coil 4 with coil 2. Started the car and now I get the P0300, P0303 and P0304 with the CEL on falshing and then solid. The CEL came on and disappeared when I got the P0304 only. The code was stored but, no CEL. Idling is a bit rough. Seems to run great when it's first started, then when it warms up it goes to crap. The car ran great since I bought it. FYI, I bought the car but don't have it on the road yet because DMV is closed until further notice. But, while refreshing the car, it ran great. The only thing I can think of is either fuel (the car is on E but, I added a gallon) or it's exhaust related. Would the higher flow of exhaust cause this?
 

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Discussion Starter #5
It seems it's only cylinders 3 and 4. 1 and 2 are fine, even using the coils from 3 and 4. Did I add too much oil? The oil level is at the send hole on the dip stick. Spark plugs are brand new and pre-gapped to .40.
 

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Discussion Starter #6
Just changed the spark plugs around and no change. I have the NGK R ZFR6F plugs.
cylinders 1 and 2 are fine. it's just 3 and 4. I'm stumped because I had no codes and the car ran as smooth as butter. I put plug 4 in socket 1 and plug 3 in socket 2. I put a flash light to look into the plug holes and its dry in all 4. The piston heads are a little dirty but, I'm sure spraying some water in the throttle will clean them up (Eric The Car Guy method).
I'm stumped. .
 

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Discussion Starter #7
I feel as if it's oil pan related. I put in a new oil pan with a new gasket because the PO patch welded the original pan. It was disgusting. Had a ton of RTV at the mating surfaces. I'm wondering if air is somehow getting in from the oil pan.
 

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I feel as if it's oil pan related. I put in a new oil pan with a new gasket because the PO patch welded the original pan. It was disgusting. Had a ton of RTV at the mating surfaces. I'm wondering if air is somehow getting in from the oil pan.
Would be a first in my diagnostic career lmao. I dont think that's your issue, you could technically run the engine with the pan off, shouldn't misfire. As long as you didn't replumb your intake air pipe and filter into the oil pan, the misfire is caused by something else.

If the car is missing at idle, that's an easy diagnose. Three types, air/fuel, ignition or compression related misfires.

Multiple different causes for each type, each has easy ways to perform an initial check. You also mentioned you messed with your EGR valve, I'll get to that one in a minute.

Quick check for a spark related misfire on your engine, just loosen your coil hold down bolts with the engine running at idle, leaving the coil electrical connector plugged in, and pull them up one at a time to and see what happens. Quick note, you DONT want to unplug the coil electrical connector when checking this, because modern OBD2 era ECUs are designed to cut fuel to a cylinder that has active ignition coil primary circuit faults. You don't want fuel to cut out while your checking this, so leaving them electrically plugged in and only lifting them above the plug is the easiest way to cut spark to the cylinders for diagnostic purposes.

1a) If you pull the coils up on the suspect cylinders, and it DOESNT change the running condition of the engine, meaning it still misfires the same with the coil on the spark plug or not, then there is a decent chance the misfire is spark related. But this ISNT the whole story, only part, we'll get to that soon.

1b) If you pull up the coils on the cylinders you feel are contributing to the misfire, and it starts to misfire WORSE, then that cylinder is still partially contributing. If this is your case, keep note and move on.


If you have 1a), at least three possibilities now exist:

1. Spark is occurring, but fuel and/or air is not being metered into the cylinder correctly, or at all.
2. Spark is not occurring. Since you said the engine ran fine before you did all this stuff, I would hold out on replacing coils just yet. It may not be a coil. Keep reading.
3. Compression loss, would also hold out on suspecting this since you said the engine ran fine before.


If you have 1b), at least 3 possibilities also exist and spark is confirmed to be working, with at least some fuel/air is making it into the cylinder to be burned, leading to contributing "some" power during the power stroke on that cylinder.

1. Fuel/air ratio is no longer correct, "MAY" be due to your air flow mods but highly doubt it,
2. Compression is weak, could be due to improperly adjusted valve clearance (did you readjust valves when you replaced the VCG?) or worn cylinders, rings, burned valves, etc, although UNLIKELY due to you saying that the engine ran fine before.
3. EGR is flowing into the cylinders when it shouldn't be. Since you said the engine ran fine before you did all this stuff, I would seriously consider rechecking EGR valve and passages.

I will provide a bit of backstory on the EGR system built into this cylinder head. The EGR valve used on this engine is KNOWN for staying partially open due to rocks of carbon buildup breaking off and holding the pintle open. This causes EGR to flow into the cylinders when it shouldn't. In most cases, this would affect all cylinders evenly, and the misfire would seem random. But because you report that the misfire seems isolated to 2 of 4 cylinders, this could be caused by the EGR passages in the cylinder head being selectively stopped up, flowing into only two cylinders and not the others.

These heads and intakes SUCK to clean carbon out of, and if you haven't seen the EGR passages in this engine before, the likelihood of having EGR flowing to two non-companion cylinders is likely due to the design. See below:

136520


EGR gases come from the exhaust manifold side of the head, with passages cast into the aluminum piping exhaust towards the EGR Valve. The EGR valve is the metering device for exhaust gases. If the valve gets stuck open due to carbon falling out and holding it open, all of a sudden EGR gases can flow towards the intake freely with no control.

The Intake Manifold EGR passages:

136521



With the gases entering the manifold next to #4 cylinder, they travel along a common cavity to the middle of the intake manifold, where they meter into cavities near cylinders 1/2, and 3/4 where the gases themselves flow into cast/machined port openings into each runner that allow the EGR to be drawn in and mix with the intake charge of each cylinder. Companion cylinders on 4 cylinder engines with 1-3-4-2 firing order are 1/4 and 3/2. You can see with this EGR design if carbon buildup blockage only affects one side of the intake manifold cavities, you could have misfires occurring on non-companion cylinders.

Easiest way to check for excessive EGR flow is to pull the valve and do an inspection. Make sure gasket is the correct way, make sure the EGR valve pintle isn't OPEN when you remove the valve, it should be CLOSED and SEATED. If it isn't, shake the valve and see if you can hear a rock of carbon jiggling inside. If you do, just get it out of there and put it all back together and see if the misfire went away.

If misfire is STILL THERE on companion cylinders, you can build a makeshift block off plate for your EGR valve using a pop/soda can. Just cut a piece of aluminum out of the can with scissors and two holes in it for the EGR mounting studs/bolts, leaving the EGR passage holes blocked, then tighten the EGR valve back down on top of it. That will fully close the flow of EGR, allowing you to see if maybe your EGR valve failed open. Those EGR valves have a reputation of going bad.

We will stop diagnostics here. Do this and report back with the results. See if you still have the misfire after all this. If so, we will continue.
 

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Discussion Starter #9
I appreciate your time and the information. Very informative. I will inspect the EGR and cap it off and test. I will let you know.
 

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Update: I sealed off the EGR with a cut soda can but, there is no change. I am not sure what to look for by sealing the EGR. I also inspected the EGR and it seems fine. The pintle I think it's called is closed and nothing is rattling inside the EGR. And there was no error code for the EGR however, I did a live scan and I noticed the FuelSys1_OL_Fault was showing. Not sure if that's related to misfires.
 

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Discussion Starter #11
Just started the car again to see how it behaves and now I'm getting a P0134 error sensor 1 bank 1. That's odd because the O2 sensor is plugged in and nothing else has changed except blocking off the EGR valve. Ever since I added the header and exhaust, all this started. The car was absolutely fine before. And the car hasn't been driven on the road. I bought the car and has been sitting because DMV is closed. So, I decided to give it a tune up, refresh the exhaust, headers, spark plugs, oil pan, and VCG. I wanted a little bit more pep for my 60 miles commute, to and from work.
 

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Good on your EGR system checks. Glad you checked and didn't find anything.

Just out of curiosity, have you driven your car yet and see what happens off throttle? Does it drive fine, yet only has this issue during idle?
 

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I bought the car about a month ago but, haven't put it on the road because DMV is closed and I wanted to refresh the car prior to putting it on the road. I haven't had the chance to drive it on the road, just up and down the driveway, roughly 10-15 ft. Mostly revving the engine throughout the month. I should have left well alone. What doesn't make sense is, yesterday when I started the car, there were no codes. After it warmed up only the P0304 appeared but, no CEL. Then shut it off and started it up again. The CEL flashed, then went solid, then disappeared. After the third start is when the three codes appeared. Today, the same three codes were there, along with the P0134. It seems as if something is loose causing the codes to appear and disappear and now the O2 sensor no activity detected? I didn't mention that I have the infamous light flicker at the headlights, dome and cluster. The battery dies if the car isn't started in a few days. And the car was recently inspected and passed. Had no codes when I bought the car.
 

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I decided to clear the codes and continue monitoring. The codes did not come back. I started the car several times and still no codes. I'm not sure if it has to be driven a certain amount of miles in order for the misfires to show up but, I assume the codes will appear immediately if there are misfires. No CEL. No P0134. It's very odd. I'm wondering if it's because of a weak battery. As I let the car idle, revved it to 5k here and there and let it warm up, the battery obviously is charging but, even when the battery died prior to replacing the header and exhaust, I never got a CEL. So, I'm at a loss.
I'm going to restart it one more time to see if the codes come back. I want it to cool down for a bit.
 

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Well, I had the car on ramps the past two days and there wasn't any oil on the ground. After wiping the codes and starting the car a couple of times and the codes didn't come back, I decided to take it off the ramps. Sure enough, there is a small puddle of oil on the driveway. I put the car back on the ramps, looked under and the oil is seeping from the back seam and above the transmission mount. Funny how it did not leak since I put the pan on and the car was started many times. Should I just get rid of the gasket and use RTV?

I can't drive the car because I haven't transferred the plates from my BMW to the civic yet. Bummer.
 

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Discussion Starter #16
Does anyone recommend I use RTV for the oil pan or stick with the gasket? I'm not sure why the gasket is leaking all of a sudden. It's a new pan and gasket.
 

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it needs to have a gasket ..

did you put RVT in a thin layer on the flat and a blob on each corner of the gasket?
 

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No I didn't. Stupid me. Now I have to drain the oil, pull the pan off and start all over. The PO had a ton of RTV all around the seams of the old pan. Here's a pic of what the PO did to the old pan. They Frankensteined the poor pan. They even put some weird sealant around the entire pan! That's why I decided to buy a new pan. I noticed there are a few bolts that hold the pan and there are mostly nuts. Do the bolts have to go in a certain hole or does it not matter?
 

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