Honda Civic / Del Sol (1992 - 2000) EG/EH/EJ/EK/EM1 Discussion

Dreaded P1399. I'm at Wit's End. Need Help.

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Old Nov 22, 2025 | 10:36 AM
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Default Dreaded P1399. I'm at Wit's End. Need Help.

PATIENT:
2000 Honda Civic LX USA 4dr. [D16Y7] 85K mi.
SYMPTOMS:
Very rough idle when warm. Hesitates bad on pull away.
TEST RESULTS:
Pending P1399 (Honda Code for Random Misfires). No other codes now but have seen P0300 to P0304 when the problem started.
Runs and drives well warming up, but once the idle comes down to 735 RPM, we get sporadic misfires, maybe 40 per minute, very random in groups of 2 or 3 even 5 in succession. Gets worse the longer it idles. Also hesitates bad at pull away from a stop when warm. No smoke in the exhaust just random sputtering sounds. Not safe to drive, almost stalls out, it's so bad.
INSPECTIONS:
• 4 NGK (ZFR5FGP-Platinum) plugs (3 years old), inspected and cleaned. Gaps were .043". Right on. Normal condition for 15K mi. Spark Plug chambers looked spotless.
• 4 SP Wires (3 years old also), inspected and cleaned. No signs of spark escape. Rerouted in case of any cross fires.
• Distributor Cap (3 years old). No signs of spark escape but replaced as most probable cause for random misfire. [One of the three cap bolts have been broken off long ago, but the cap fits tight with two.]
• Ignition Coil (original). Removed and showed signs of swelling and discoloration. Replaced with new coil.
• Ignition Control Unit (original). Replaced with new at same time. No help either.
• PCV Valve, Grommet and Hose replaced because the engine has lots of oil everywhere. Tough job.
• Replaced Valve Cover Gasket and checked Valve Lash on all 16 Valves. All within spec. +/- .001". First time ever checked. Wow!
• Removed Timing Belt Cover and inspected Timing Belt. Looks great.
• Checked Crank/Cam Shaft sync, right on the white TDC mark.
• Check Idle Timing with ECU disabled, near the Red Middle Mark.
• However I noticed that for each misfire the marks moved back (toward firewall) temporarily meaning each misfire was a few degrees EARLY. Timing Light on each wire did not show any missing sparks.
• Throttle Body to Intake Manifold Gasket changed because I had the TB off to get to the PCV from the top.
• Inspected Vacuum Lines (original). Can't find any breaks.
• Radiator is full.
• Gas tank full with fresh Ethanol-Free 87 Oct.
• ECU reset each time the battery was disconnected while working on engine.
• Battery: 3 years old, 12.5 VDC, no load.
• Fuel Filter: Replaced because it was time.
• SCAN Idle Speed: 735 RPM, drops down to 670 RPM when sputtering.
• SCAN shows MAP at 14.8 psi engine off, 4.6 psi at idle. Presume that is working OK.
• Compression Test: COLD/WOT: 180/170/180/175 psi, Nice numbers!
• Engine has no EGR Valve. Nothing to clean there.
• SCAN shows ST Fuel Trim varies around -2.5%.
• SCAN shows LT Fuel Trim pretty steady at -1.6%.
• SCAN SparkAdv: 10º-12º at idle.
• Idle Air Control: Not inspected yet. Doubt this is the problem.
• Just noticed Oil Level on Dip Stick is 5/8" over the MAX hole (see image). Recent Oil/Filter Change before problem! Could overfill cause misfires? Seems unlikely.
• After 15 minutes of idling the ECU finally lit the CEL and stored 3 codes: P0300, P0301 & P0303 plus still pending P1399.


I need HELP for next step! Not safe to drive.
TIA. Time for coffee!
Florida Rich



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Old Nov 23, 2025 | 02:07 PM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

Check the indexing on the distributor. If it only runs right when it's fully retarded, but stalls when the a/c get turned on, your timing belt may have skipped a tooth.
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Old Nov 23, 2025 | 04:44 PM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

Originally Posted by pimpachu
Check the indexing on the distributor. If it only runs right when it's fully retarded, but stalls when the a/c get turned on, your timing belt may have skipped a tooth.
Checked the synch between the crank and the cam shafts, as noted above. Using the marks on the BACK of the cam pulley to the block surface and the TDC marker on the crank pulley are in synch with each other. We have not used the A/C in years. There is no A/C belt either.
Also moved the Dizzy forward 2 degrees, back 2 degrees and back to where it was. Had no affect on misfires.

UPDATE: Siphoned out 1 quart of oil from the crankcase via the Dip Stick Tube. Then took it for a long ride. At idle, still misfires and hesitates but only when warm. Runs fine at 20+ mph. On the way home my SCAN popped a new code: P505. That's great info. Tomorrow the TB and IACV comes off for a look-see. I may be on to something here.

Thanks for your suggestion pimpachu.

Florida Rich
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Old Nov 24, 2025 | 09:23 AM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

UPDATE: With a pending P505 code from yesterday, I replaced the IAC Valve today. Was not that dirty. TB was clean. Cleared the code and took it for a ride. Acts fine for the first 3 miles until it warms up. BUT THE MISFIRES AND HESITATION ARE STILL THERE. VERY BAD IDLE BY THE TIME I GOT BACK HOME. At one time I could feel about 7 misfires in a row, then sporadic groups of 2 and 3 at a time. No Saved or Pending Codes today.
What am I missing here?

Florida Rich
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Old Nov 24, 2025 | 11:40 AM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

put new ngk plugs in. copper. no platinum
get rid of those plug wires. use NGK or OEM
new OEM cap and rotor
OEM ignitor and coil

honda ignition systems are notoriously finicky

ive seen cars on the dyno with champion spark plugs and parts store wires
no power and breaking up at high rpm.

changed plugs to ngk copper and put some used OEM wires that were found in the corner of the shop
makes power now and no breaking up at high rpm

if that doesnt work then check the valve adjustment

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Old Nov 26, 2025 | 05:12 AM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

UPDATE: Returned to OEM Cap, Coil and Igniter. New NGK BPR4ES Copper Plugs like you suggested. Test drive, runs fine for the first few miles while warming up. Once the ECT gets to 180 deg. it starts acting up. Misfires bad. At a stop sign, I'm afraid it'll stall before I get across the intersection. My Max ECT is 190 deg. so I'm not over heating. Pending P1399 came back by the time I got home, but no stored codes. Valve clearance was check before. All 16 valves are right on. O2 Sensor #1: 0.1 to 0.9V rapid oscillation. O2 Sensor #2: varies slightly 0.45 to 0.7V .
Is it possible I have an air pocket in the cooling system? My radiator is full when cold.
Someone out there must know what to check next.
TIA.
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Old Nov 26, 2025 | 05:26 AM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

Have you checked fuel pressure? Maybe the regulator or the pump are bad.
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Old Nov 26, 2025 | 07:24 AM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

Have you checked the coolant temp sensor?
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Old Nov 26, 2025 | 07:35 AM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

Originally Posted by Z31freak
Have you checked fuel pressure? Maybe the regulator or the pump are bad.
Excellent idea. I was getting to that place eventually.
Low fuel pressure would cause lean condition BUT the car does perform nicely at 40 mph and during warm up at 1200+ rpm, when demand is higher, so low fuel pressure does NOT make sense. On D16Y7, I think there is no port with a Shraeder Valve, so checking with a pressure gauge is not easy on this engine. I'll have to buy a Fuel Pressure Gauge too. Might be cheaper to buy a new Regulator. Holiday weekend in the way, now. Car's been down for 2 weeks.
Another possible is - it needs a whole new Dizzy if the timing is wandering at idle. See my comment above about Ignition Timing with the Timing Light. Flash jumps from 16 deg. BTDC, to like 20 deg. BTDC when the misfire occurs. Very next flash is back to 16 deg. BTDC. Curious about that.

Tnx, Z31freak.
Florida Rich
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Old Nov 26, 2025 | 07:38 AM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

Originally Posted by speedooo
Have you checked the coolant temp sensor?
No but my SCAN shows ECT is 90 deg. F when cold and rises to 190 deg. F when fully warmed up. That is the Temp. Sensor.

Tnx, speedooo.
Florida Rich
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Old Nov 26, 2025 | 09:18 AM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

Originally Posted by Florida Rich
No but my SCAN shows ECT is 90 deg. F when cold and rises to 190 deg. F when fully warmed up. That is the Temp. Sensor.

Tnx, speedooo.
Florida Rich
Interesting.

Have you touched any wires? I mixed up the o2 signal and coolant temp wires once and I had a similar issue. One is red/white and the other is white/red.
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Old Nov 26, 2025 | 12:04 PM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

Originally Posted by speedooo
Interesting.

Have you touched any wires? I mixed up the o2 signal and coolant temp wires once and I had a similar issue. One is red/white and the other is white/red.
No, I am careful about disassembly and reassembly. I even take photos of the component before removing it. Plus every sensor has a different connector. This is NOT to benefit service people, they do it to prevent manufacturing errors during vehicle assembly on the line.

My SCAN tool allows me to do a "Reset Factory Default" to the ECU. Thinking of trying that and have the ECU be "re-educated".
Thoughts?

We're off to "Pie Night". Thanksgiving Eve custom. "Eat dessert first! You'll be too full for it tomorrow."
Florida Rich
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Old Nov 26, 2025 | 07:34 PM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

Does your scan tool show short term and long term fuel trims ?
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Old Nov 27, 2025 | 05:38 PM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

Originally Posted by JRCivic1
Does your scan tool show short term and long term fuel trims ?
Yes. See my first post:
• SCAN shows STFT varies around -2.5%.
• SCAN shows LTFT pretty steady at -1.6%.

FPR on order.
Florida Rich
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Old Nov 27, 2025 | 06:28 PM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

Here I thought "Restore Factory Default" meant reset the ECU. It means it puts the SCAN tool back to it's original out-of-the-box settings.
My Foxwell NT301 SCAN may not be able to do any resets to the ECU.

Florida Rich
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Old Nov 27, 2025 | 08:05 PM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

If your combined short term and long term fuel trims are about -4%... a new FPR will not solve your issue.
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Old Nov 28, 2025 | 06:46 AM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

BACKGROUND: This 25 year old reliable Civic (D16Y7) is owned by an 85 year old lady who bought it new 25 years ago. It's her only means of transportation. She now lives on just Social Security and can't afford to bring it to a Honda dealer for service because they tell her: "Oh, you need this and this and this and this done at $2,843!". So I, and another friend of hers, are BYMs (Back Yard Mechanics) and work on her car for her, the best we can. The other BYM was stumped with the misfires. Now, so am I. I am used to working on my fun car, that I've owned for 50 years! It's a 1942 Chrysler Royal 9 Passenger Sedan. Chrysler made just 26 of them before the war. All original! It's 4 years older than the Honda Motor Co. and just 2 years older than me. Here's "Betsy". [Do you know how to set the "Dwell Angle" on the Points ? ] Help me find why her Civic has random misfires only when it's idling warm and on pull away. TIA. Florida Rich.
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Old Nov 28, 2025 | 10:25 AM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

IDK if this applies to your Honda or not, but here goes my 'tip': My 94DX OEM came with splitfire 'V' copper tip NGK spark plugs. I got fancy & 'upgraded' to platinum ('V' not an option) but it didn't run very well. Over a couple yrs I changed out 3 more sets of platinums, none of those worked well either (The definition of insanity 🙄 ). Bosch platinum version of the same part# ran worse than the old splitfire 'V' copper tip that were badly worn & rounded off. I was convinced there was something else wrong but found nothing. I spent a lot of $$$ those danged Bosch platinums too, which were the only plats available back then.

One day I read a random post saying platinum plugs made their Civic run like crap & they switched back to the split copper 'V' tip plugs that were original to their vehicle & 'viola', it ran like a champ. I searched for more info @ it & people were complaining about Bosch platinums but that might have been because that was the only brand available at parts houses back then.

I installed a new set of the original NGK splitfire 'V' tip copper plugs & my old girl purred like a kitten & ran like a scalded dog, no hesitation, no stumbling. Moral of the story: use the same type of plug & part# it came with, with the exception of the best heat ranges that may vary by your location. I wasted a lot of money on platinum plugs & time chasing down a problem I created with my 'upgrade' 🙄 Swap the platinum plugs to original OEM that it came with new before loading the parts cannon.



Originally Posted by Florida Rich
Checked the synch between the crank and the cam shafts, as noted above. Using the marks on the BACK of the cam pulley to the block surface and the TDC marker on the crank pulley are in synch with each other. We have not used the A/C in years. There is no A/C belt either.
Also moved the Dizzy forward 2 degrees, back 2 degrees and back to where it was. Had no affect on misfires.

UPDATE: Siphoned out 1 quart of oil from the crankcase via the Dip Stick Tube. Then took it for a long ride. At idle, still misfires and hesitates but only when warm. Runs fine at 20+ mph. On the way home my SCAN popped a new code: P505. That's great info. Tomorrow the TB and IACV comes off for a look-see. I may be on to something here.

Thanks for your suggestion pimpachu.

Florida Rich

Last edited by Plutonodian; Nov 28, 2025 at 10:46 AM. Reason: Edited: ignore the # + random numbers added after 'insanity' - supposed to be an emoji + parenthesis
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Old Dec 2, 2025 | 01:44 PM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

• PROBLEM SOLVED: While waiting for new plugs to arrive, I tested the 3 year old Auto Battery and found it to be below ideal. Didn't seem to hold a full charge very long, although I had no problem starting the Civic. So a new Interstate 51R 500 CCA Wet Battery ($124) was installed. Since there are YouTube videos that suggest P1399s might be caused by poor power to the ECU, I immediately took her out for a run with the new Battery in place. As usual, starts on the first revolution and pulls away fine when cold. By the time the ECT was 180 deg., the misfires started again. No Pending codes yet. Limped home. O2 Sensors working fine. MAP correct. Fuel Trims OK.
• The next day, 4 new NGK ZFR5F-11 (Stock #2262) (OEM - Copper) Spark Plugs arrived. I removed the 4 Plugs that were in it. They are also NGK ZFR5F-11s. [See the photo.] They replaced 4 NGK Platinum 3 year old Plugs, a while ago with no change. They look hardly used. Little carbon, no cracks or spark tracks. They are dark gray as expected and had been wire brush cleaned a week ago. They look fine and all pretty equal.
* Installed the spanking new shiny NGK Copper 2262 Plugs, check the gap at .044", lots of dielectric grease, torqued to 20 ft-lbs and I was off. Well, low and behold, the new Plugs did the trick. Ran for a half hour, no mis-fires, no codes. Let it sit and idle in gear and out of gear for a while. Purrs like a kitten. Who-da thought?
• PROBLEM SOLVED: Yippee!

(Thanks to all who replied. The old lady has her old car back.)

Florida Rich

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Old Dec 13, 2025 | 08:16 AM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

Glad you got it fixed. I'm sure she's happy. I wonder if your first set of NGK's were counterfeit. Personally I won't buy spark plugs from Amazon or rock auto. I always go to the dealer or at worst to Autozone.
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Old Dec 19, 2025 | 02:46 PM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

Being an 'old lady' myself, I'm happy my little story about spark plugs may have helped you get your old lady's Honda back on the road. I am 💯 sure the Bosch platinums I used were not counterfeit though. They're just the wrong plugs to use. Unlike the copper Vs in my Civic that you check & adjust the gap, the instructions on the Bosch platinums say they come pre-gapped & to not try to adjust them. Ditto for cleaning or brushing them. Pretty sure the Vs split the fire, making the explosive combustion in the chamber complete at each fire.
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Old Dec 23, 2025 | 07:49 AM
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Icon5 Re: Dreaded P1399. I'm at Wit's End. Need Help.

It's BAAAACK! Owner reports to me today "it's sputtering again!" So I got in my sleigh like a good Santa, woke up Rudolph and his troops, zipped over there and brought my SCAN TOOL with me. Sure enough, after 3 weeks of running fine with new Copper OEM plugs, the D16Y7 now decides to go back to random misfiring. I got P0300, P0301, P0303 and P1399 (pending). Hmmm! Same exact codes as Post #1. No time to pull the plugs now but we'll have to see what they look like after Christmas. The car runs too rough for safe driving, so that puts a damper on her Christmas.
Need more suggestions. TIA.

Florida Rich...
Happy Holidays all...

Last edited by Florida Rich; Dec 23, 2025 at 08:20 AM.
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Old Dec 23, 2025 | 06:29 PM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

Ignition components are important. SP sounds like some Amazon junk brand of spark plug wires. So if you've replaced the coil and icm with non oem parts you'll have issues.
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Old Dec 24, 2025 | 05:34 AM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

Originally Posted by Chrisfrom1986
Ignition components are important. SP sounds like some Amazon junk brand of spark plug wires. So if you've replaced the coil and icm with non oem parts you'll have issues.
Thanks for your post. My head is thinking: Replace the SP wires with NGK branded. I'm going to check the inside of the DistCap too. The Plugs are genuine NGK both what came out and what I put in.
I also noticed when I started the car yesterday, that the exhaust is much louder than before. Sounds like a hole is starting in the exhaust somewhere. Could that contribute to misfires? I never got any error codes for Cat-Con being out of bounds with the O2 readings. Only codes were for the P300s.
Santa has other chores in the next few days.
Florida Rich
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Old Dec 24, 2025 | 08:03 AM
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Default Re: Dreaded P1399. I'm at Wit's End. Need Help.

Originally Posted by Florida Rich
UPDATE: Returned to OEM Cap, Coil and Igniter. New NGK BPR4ES Copper Plugs like you suggested. Test drive, runs fine for the first few miles while warming up. Once the ECT gets to 180 deg. it starts acting up. Misfires bad. At a stop sign, I'm afraid it'll stall before I get across the intersection. My Max ECT is 190 deg. so I'm not over heating. Pending P1399 came back by the time I got home, but no stored codes. Valve clearance was check before. All 16 valves are right on. O2 Sensor #1: 0.1 to 0.9V rapid oscillation. O2 Sensor #2: varies slightly 0.45 to 0.7V .
Is it possible I have an air pocket in the cooling system? My radiator is full when cold.
Someone out there must know what to check next.
TIA.
The reason why its runs good until its warmed up is because the engine is in open loop. Meaning the computer is controlling the engine without feedback from any sensors. Once its warmed up it goes into closed loop, relying on sensors to tell the computer what the fuel values should be, Find out what is changing when the computer goes from open to closed. Do a search for P0300/1399
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