There are two causes of a surging idle: mechanical and tuning.
The idle valve gets stuck fairly easily, particularly if the car has not been used for several weeks. Pull the idle valve off the throttle body (4 phillips screws on the bottom), remove the electrical part of the valve (2 screws) and clean the valve with solvent until it rotates freely.
As far as tuning goes:
1. Make sure your TPS is set so that it is between -1 and 0 at idle. It has a security screw so it is a pain to adjust. You can tap it carefully with a punch if you just need to tweak it a percent or two. (be careful - Honda doesn't sell the TPS seperate from the throttle body!)
2. Reduce the ignition advance on the 0 degree map in the first 5 columns up to (and including ) 1500 rpm (approx idle area). You may need to reduce to ignition to anywhere from 15 to 20 degrees.
3. Reduce idle speed slightly (850 - 950 rpm usually works).
4. Datalog and check that the cam angle is zero at idle. If not, check #1
5. Alter the idle valve duty cycle adjust slider value. Rev the engine to about 3000 rpm and release the throttle quickly. If the rpm drops below the idle speed and then recovers, then move the slider to the right. If the rpm drops to 500 above idle speed and then goes slowly down to idle speed, move the slider to the left. See below about how this is affected by the ECU idle learn.
Note that after uploading a calibration the ECU takes a little while to learn the correct duty cycle for the idle valve (even if the upload is a very small change it resets the ECU's memory). If the car is hot then this learning process happens in a couple of minutes, but if the car is cold the ECU won't learn until the car is hot - and in the meantime, the engine sometimes stalls with large injectors. The trick is to not increase the idle speed too much to prevent the engine stalling if the engine is cold, because it will fix itself once the ECU learns the idle.
If you get a slight misfire at idle once the car is warm, slowly enrichen the idle target A/F ratio.
