I have a '99 Civic DX, 5-speed, and for the last couple months I've been having trouble with cold starts. The engine turns over fine and fires, but it starts really rough and sounds like it's running on 2 or 3 cylinders. Many times it dies and I have to start it again. Giving it gas helps a little, but the rough running becomes even more pronounced, like it's missing a cylinder or two. After running rough for about 5 or 10 seconds, it suddenly recovers and runs smoothly from then on. After it starts running, the engine idle does seem to me to be a bit low for a cold start, but it is summer and I can't really tell what it should be. Warm starts are fine. I've tried changing the plugs and wires, and cleaned the cap and rotor (since they are relatively new), with no change. This problem is an annoyance for now, but I fear that come winter, I will have even more trouble starting in the frigid mornings.

I also am having a possibly unrelated problem with the engine overheating on this car. This also happens only on cold starts, and only occasionally (maybe twice in a week). After a cold, difficult start, I'll be driving down the road for about 5 minutes, and the temperature gauge will start rising past normal. I turn on the heat inside the car, and only cold air blows out. I'll be driving at normal or highway speeds, with the engine running perfectly smoothly, mind you, and the temperature gauge will continue to slowly climb to almost the red, when suddenly it drops down to normal, and at the same time, I'll start to get heat through the vents, and everything is fine after that. After this happens, I need to add about a cup or two of coolant to top off the radiator. I'm not sure if this is related to the rough starting issue, but it may have started around the same time. Mind you, I am careful not to peg the temperature gauge at the red. I'm not sure how safe it is to run the engine with the temperature close to the red, but this has been happening for at least a couple months, once or twice a week, and each time, the temp dropped to normal before it got to the red. I've tried flushing the cooling system several times (flushed the block, heater core, and radiator separately) with no sign of obstruction or clogging. I also replaced the thermostat, and checked the compression of the cylinders (all 4 are around 140psi).

I would appreciate any ideas on what I should check next.

 

Maybe a leak in the head gasket letting gas out of the cylinders to displace the coolant. Heater not working almost always means the engine is not completely full of coolant.

Let it run rough for a short time, then before it smooths out shut it down and take the spark plugs out. See if any of them are wet.

 

After a few seconds of running rough, the engine recovers and runs smoothly. I did take out all of the spark plugs today after the engine had been running (just before I tested the compression), and all of the spark plugs looked about the same; none of them were wet or black.

 

You need to check before it starts running smooth. Once it is running smooth, the plugs will clean themselves up.

 

is there any cel???
have the codes been pulled??

 

I just checked the plugs after letting the engine run for just a few seconds; they all look about the same...none of them are wet.
The check engine light does come on once in a while; I forgot to mention that in the original post. I took it to Autozone a couple of times; the first time it showed random cylinder misfire, and the second time it said cylinder #2 misfire.

 

do you have any coolant loss? does it smoke?

 

Yes, I changed the plugs and wires, and I cleaned off the cap and rotor because they are relatively new. No change.

 

any moisture in cap? or any cracks or residue build up on contacts?

what about coolant loss? does your car smoke?

 

The car doesn't smoke. There is some whitish smoke coming from the exhaust on colder mornings, but it clears up and it doesn't seem to be anything unusual.
I usually don't lose any coolant, but after an overheating episode, I can add a cup or two of coolant to top off the radiator.
There is no moisture in the cap; the seal is good. There was residue on the contacts in the cap and rotor, but I cleaned them off. I didn't look for cracks, but there was nothing obvious.