I know my car (94 civic ex) has a FITV (fast idle thermo valve) located right under the throttle body. This controls idle somewhat, and is prone to get clogged up. Even if it is not, if there is air inside of it, it will make the car idle roughly.

Here is something easy to try that fixed the same exact issue for me:
When car is !COLD! take off radiator cap.
Start the car up, then slowly add coolant into the radiator. As you are filling it up, your car should start to idle more normally.

Let me know how this works.

Also try to search for the fitv on the forums i know there is a how to on cleaning that out somewhere... I am not exactly sure your model has it however.