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"S" usually refers to the speed sensor This sensor translates your MPH and RPM . If the tranny is behaving erratically, try to troubleshoot by pulling the codes from the on board diagnostic unit (You can usually do this with a paper clip after you locate where the connector is located). Refer to Honda codes for your model They will blink on your dashboard and you count the number of blinks that correspond to the Honda engine code. the "S" light is sort of like the check engine light, except it refers to tranny problems only....there is a cable speed sensor cable, that is attached to the top of your tranny and runs to the back of the odometer.
Have you had the engine control computer scanned for fault codes that might explain what this is? Do that first. You will need to buy a code reader for a OBD2 electronic engine control system, the diagnostic connector is in front of the driver under the dash.
If you have a check engine light get the code. It may not tell you exactly the problem but it will give you a direction to look at. Where I live many auto parts stores will give you the codes for free.