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Before anyone asks, yes I've read through the info for a rough idle. I don't think that's directly related to what I'm experiencing.

My friend's 01 civic ex has been hispaniced out (before he bought it... he knows nothing about cars) and among it's many problems it's main running concern is a stumble or hesitation. No codes, the only intermittent code is for the front O2 sensor's heater and that won't cause any running issues, especially once the car's reached temp. The code wasn't even triggered when I worked on the car the other day. It used to hesitate and sputter whenever he would leave from a stand still, then randomly off idle when trying to get down the road (often after shifting to the next gear). The throttle body had been cleaned by a shop about a year ago, and I cleaned it again the other day, installed new NGK plugs and did a seafoam induction service on it.

The problem has seemingly gotten much, much better, though it still exists. I tried pinning it from a medium launch and around 4500 or 5000 it stopped pulling and sputtered for a second, then caught up and pulled to redline. Again, plugs and induction service did help in some way. Monitoring the car at idle it runs fine to the naked eye, then occasionally chugs and sounds like it may stall, then smooths out. Watching it on my scan tool I can see the long term fuel trim stays at -3.1 at idle, while short term fuel trim fluctuates constantly. It ranges from about +15 to -15, and you can watch it swing from one to the other slowly. When it reaches about -10 or -12 that's when the car chugs and sputters, the ignition timing jump from about 0 or 2 degrees to 15, then as the engine smooths out it returns to 0 and short term fuel trim begins it's searching cycle up to +15 and back. Watching the O2 sensor readings shows a direct reflection of the short term fuel trim: when it goes positive the O2 reads about a full 1.000 volt, then when it shows negative short term fuel trim the O2 reads about .007

Really not sure what would cause such a predictable and reoccurring condition. I dont think it's an idle learn issue, because it happens off idle and it's not constant. I'm certainly open to the idea of it being a vacuum leak, I just need to find some way to smoke test the intake, since it's not a steady issue. I've also read somewhere that the vacuum ***** are a common source of a vacuum leak on these cars, but I feel like if it were something that simple it would be a more steady issue, and it wouldn't flash up at random at mid to high RPM. I figured I'd ask you guys, since I'm sure you know a million times more about civics than I do. I always encourage troubleshooting using info from enthusiast forums. That's the fastest and cheapest way to get things fixed. So, let's hear what you've got.

 
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I had the same problem in my 98 EX, other than the splutter while running it also spluttered while in drive position pressing on the brake while waiting at a light. What I did was advance the timing just a bit and when the car was hot sprayed some brake cleaner inside the hole in the throttle body that leads to the IAC sensor and so far the splutter has stopped and idles perfect when waiting for a stop light. Hope this helps

 
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checking for vacuum leak is easie while car is idling spray starting fluid on every hose under hood slowly and through if no changes in idle speed then could be just a bad alternator bearing making it sound bad or vibrate