I have a 2003 Civic Ex Automatic

Car experiences intermittent cooling issues and a choppy idle. Car starts up great and runs fine for around 2-3 minutes, then the idle starts getting choppy and the car hesitates. Also when driving for more than around 10 minutes or sometimes up to 40 minutes, the car will start to dangerously overheat, I always stop before it does, but the weird thing is it never overheats when sitting and running, and I do notice the cooling fans turn on as they should. I’ve tried replacing the thermostat and it didn’t fix the issue still the same, sometimes overheats sometimes doesn’t, and tried replacing the engine temp sensor, and still no luck. Also tested for BHG but no signs or symptoms of a BHG. Car loses coolant over time and I have no idea where from as I haven’t seen or found any leaks, and I did a thorough bleeding of the coolant system, My next step was going to be replacing the waterpump cause the flow of coolant in the bleeder funnel seems to be super choppy and although the bubbles in the system do preside, the coolant will start to splash wildly when bleeding the system.

TLDR;
Problems:
intermittent overheating only when driving
jumpy/unstable idle
loosing coolant over time (I think)
choppy flow of coolant when bleeding the coolant

parts replaced so far:
thermostat
Engine temperature sensor

 

How did you test for a blown head gasket? That sounds like what you have.

Anyway, try a radiator pressure test. Honda uses plastic radiators; they are prone to splitting where the plastic joins the aluminum. In any case the radiator should hold pressure equal to the cap pressure.

A radiator pressure test will also detect a blown head gasket.

 

If you got a cheapo thermostat it may not be good , same with the temp sensor . I think it has 2 , one for the gauge and one for the fans .. If you're serious buy an OEM dealer parts , From my experience it's the only option . A compression test wouldn't hurt , What do the plugs look like

 

Did you check the sticky on the 01-05 civic thread?
Most likely it is gonna be a head gasket issue, these gen civics are notorious for this problem. They spill out coolant from the overflow bottle and eventually it goes dry and over heats. The solution is to change the head gasket and have the head checked for warpage.

 

Ditto on the head gasket as the previous posters have said. I dicked around for weeks trying to solve an intermittent cooling problem to no avail. I could not determine a head gasket leak with a compression test or rad test. But it slowly got worse and replacing the head gasket solved everything. Engine only had 180 k miles on it and the machine shop I took the head to only checked it for warped and cleaned it . He said it did not even come close to needing the valves reground. Runs as it should now.

 

I drove a 1.7 with a weak head gasket for months till it finally gave out . Even then it would run , poorly but you could drive it . Great engines , good cars .