Let's say I'm getting off the freeway, I press the clutch, shift out of 5th to neutral. At that moment my Civic DX would usually drop to about 1000 rpm at idle. For the past month it drops too low, somewhere between 200 to 400. It drops and the car feels like it's about to turn off but jumps back up to 600 rpm at idle. There's been a handful of times where it fully shuts off even while the car is moving. When the car is cold it works great with no problems, idle is at 1000 rpm. After driving 10 minutes and the car is at normal temp, the problem starts occurring, idle then drops to 600 rpm. My car is stock other than CAI and exhaust. Manual transmission. I've tried fuel injector cleaner, changed my spark plugs, cleaned my K&N air filter.
When the throttle body becomes a little worn, it is possible for the butterfly valve to close too much for a steady idle engine speed. The ECM then tries to compensate by opening the IAC more than it is designed to under normal conditions. This can cause stalling and unsteady idle. There will be a screw on the throttle body that allows adjustment of minimum throttle. Try adjusting the screw to open the butterfly valve a little.
You may already have looked at this since it sounds like you've been under the hood quite a bit, but take a good look at your air intake hose too to make sure it's not cracked/leaking. I had a very similar problem on my 02 Protege a while back and that was the cause.
If that looks fine, can you take it to Autozone and have them check for engine trouble codes? If you have a cylinder misfire code it could also be a bad ignition coil or spark plug wire (since you already replaced the plugs and it didn't go away).