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2004 ex manual rough idle cooling problem

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Old 12-16-2016
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2004 ex manual rough idle cooling problem

A bit of history on this car - 2004 Civic EX. 1.7L Vtec. Manual transmission. I bought it at an auction for super cheap knowing it had a few issues. Those issues were:

bad intake shaft bearing, bad throw out bearing, bad CV joints, CEL threw a code which turned out to be a faulty O2 sensor. Other than that the car was in good shape and everything got taken apart and fixed using genuine Honda MTF, seals / gaskets, synthetic oil, Napa Gold oil filter, whatever coolant Honda sold me, I can't remember now what kind of coolant it was. Basically all parts were honda stock parts except the CV joint and I put a new after market clutch and pressure plate in because with 200k on the vehicle I didn't really feel like chancing when it was going to go out on me and have to pull the engine again any time soon. The input shaft bearing I read had issues, so I used an NSK I think it was. It's a german brand that my company uses a lot and had amazing reviews. Supposed to work better than the Honda bearing.

I put it all together and everything is not only fine but dandy as well. Now that the god awful clicking of the input shaft and CV joints are gone I can hear a rough idle. I go through the list posted on this site to fix idle issues and so far the only things I haven't done are injectors and check compression. New K&N air filter, cleaned throttle body (it was pretty damn clean to start with) new intake gaskets and hoses happened when I put the car back together from the transmission fix. New plugs (NGK) new wires.

Here's the part I can't wrap my head around, when it idles the heater blows cold air. The coolant levels are good, I have no coolant loss. I have an extremely slow oil loss. I don't see leaks so I'm guessing head gasket? This is why I haven't done injector check or compression check I just figured I had a bad head gasket. Now that this heating (or likely more appropriately cooling) issue is surfacing now that I'm actually using the heat I'm kinda confused.

Anyone have any thoughts?

Last edited by Elciteeve; 12-16-2016 at 12:05 PM.
Old 12-16-2016
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Re: 2004 ex manual rough idle cooling problem

when it idles the heater blows cold air.
And... heat may get a little better if you raise the RPM a bunch?
Big air bubble in the heater core can do this.
You checked the radiator and said it's full, but is it completely full to the top? It's supposed to stay completely full under all conditions.

It doesn't take much liquid loss to cause heater issues in cold weather. Less than a quart low can do it.


You can read about how to burp the cooling system.... My own preference is to use the usual burp methods, using a cooling system funnel attached to the radiator neck, half full ----- along with raising the front of the car as high as safely possible (make the radiator the highest point of the cooling system),
Raise the front wheels off the ground: put the trans in lowest gear, and rev the engine to redline several times. The significant pump pressure increase at high RPM can help push the air bubble on through the heater system.
Make sure the oil is full before you rev it up to redline too.

Next question has to be, 'How did that air bubble get there?' Low coolant level at some point, and if no external leaks are found then the typical cause is a blown head gasket. (if coolant was just replaced let's blame that for now, unless something else is discovered)

I have an extremely slow oil loss. I don't see leaks
200k? Consumption. Stuck oil rings would be my bet. Typical.
Old 12-20-2016
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Re: 2004 ex manual rough idle cooling problem

Thanks for the great info. That all makes perfect sense. Yes the air blows hot if I rev the engine up a taste. It doesn't take much, maybe an extra 300 RPM and the heat is good.

Sounds like step one is burp the cooling system, see if that makes that particular problem go away. Then wait for it to come back. If it does I have a confirmed head gasket replacement since I'll be inspecting those rings either way. But waiting it out a bit should narrow down the diagnosis yeah? If I have a bad gasket that could be the oil loss, air leakage in cooling system, and the rough idle all in one problem.

Sorry for the delayed response, my wife's car was stolen and I've been a little busy rounding up something for her to drive and now I get to repair the damage from the thief, plus fix my car as well. Yay.
Old 12-20-2016
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Re: 2004 ex manual rough idle cooling problem

It doesn't take much, maybe an extra 300 RPM and the heat is good.
How much does it cool off at idle rpm? A 'little bit cooler' at idle might be typical simply because of slower liquid flow, but 'a lot cooler' isn't right. If that makes sense.


If it does I have a confirmed head gasket
Not necessarily, but it's likely....
I rely on one particular test to prove head gasket leakage on this engine.
Find the 'overheating common causes' sticky thread, read the first post and see the 11 minute video.

If I have a bad gasket that could be the oil loss, air leakage in cooling system, and the rough idle all in one problem.
Air leakage into the cooling system--yes, but the head gasket problem won't cause oil usage, and probably not the rough idle either.

You say you can 'hear' rough idle, maybe valves need adjusted?
Old 12-22-2016
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Re: 2004 ex manual rough idle cooling problem

Originally Posted by ezone
How much does it cool off at idle rpm?
It blows cold air. Like I don't have the heat on at all.

Originally Posted by ezone
You say you can 'hear' rough idle, maybe valves need adjusted?
It's not as much a noise, so much as a feel. The engine just isn't smooth at idle like it's supposed to be. Similar to a bad plug wire that hasn't quite totally quit, or a vacuum leak. However I can't find any signs of those issues.

It could be the valves, I haven't checked them.
Old 12-22-2016
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Re: 2004 ex manual rough idle cooling problem

Sounds like you're back to an air pocket in the heater system, and maybe start with a compression test for the rough idle?
If the head has to come off, you will need to know just how deep you need to go with it.
Old 02-05-2018
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Re: 2004 ex manual rough idle cooling problem

Finally got around to fixing this head gasket (which turns out was the problem) I put everything back together with an OEM Honda brand head gasket, and a few other misc gaskets that came off along the way, including new timing belt. I checked my alignment of crank and cam before closing up the timing cover and everything looked good. I mark the pulleys and block / valve train with a paint pen and nothing moved during the disassembly / reassembly.

Now that the car is back together on first start up it didn't want to start. At all. I had to pump the gas a lot to get it to turn over properly and when it finally did start it idled like ****. Coolant loss like crazy, but I'm pretty sure it's from a hose that is now cracked or something. I will know more tonight when I take the intake off to inspect further. I'm praying it's not coming out of the head gasket. I followed the three step torque procedure per spec and everything seemed to go smoothly. My smallest feeler gauge is .002" which I could not insert under my certified flat straight edge, so as far as I can tell my heads / block are flat to under .002"

At high RPM the engine seems to run ok, but at idle, even after doing the idle relearn process, it just runs like it's starved for air, or has no oil in it or something.

Anyone have any thoughts?
Old 02-05-2018
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Re: 2004 ex manual rough idle cooling problem

Figure out where the coolant is leaking

Compression test?

Check engine light/codes?
Data list?

vacuum leaks? (a poster once broke their plastic intake manifold)

EGR stuck open?

Valve clearance adjustment correct? (I prefer setting to looser end of spec)

Did you set the head down on the floor or bench and bend the open valves?
(some valves are always open and they bend very easy)


Did you suck the liquid out of the head bolt holes before assembly? That can cause problems such as false bolt torque, insufficient clamping force on the head gasket, and fracturing the block casting.
Old 02-06-2018
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Re: 2004 ex manual rough idle cooling problem

No codes showing.

Haven't checked for vacuum leaks. Will do that.

I cleaned the EGR and replaced the gasket about 10k miles ago so I didn't mess with that, although that doesn't mean something didn't happen since then.

I cleaned out the head bolt holes as best I could, used about 2 rolls of paper towels to sop up any fluid I could get out of 'em.

I set the head on two blocks I had set up before hand so the head would be sitting like it does when installed on the engine (upright if you will) but the blocks didn't interfere with any of the valves.

Didn't do a compression test, I showed exhaust in my coolant doing a funnel test in the radiator which led me to replace the head gasket.

Haven't checked the valve clearance. Will do.

I didn't get a chance to see where the coolant is leaking from. Life happened. I took This Friday off so I will have a full 3 days to work on this (and my two other cars that need attention) over the weekend. Hopefully that's enough time to diagnose and fix all 3 vehicles.




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