A problem can occur with a vibrating expansion valve in the AC system which causes a whistling noise from the passengers vent. Replacing the expansion valve with an updated valve from Honda should repair this problem.
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Repairpal verified 2003 Honda S2000 problems
A faulty relay can cause the air pump to overheat and cause the Check Engine light (MIL) to illuminate. Replacing the relay will fix this issue.
There are known convertible top issues.
On some models the center console can lift in the rear. Trimming the padding underneath the console will repair this problem.
The S2000 is set up with aggressive alignment settings and soft tire compounds to enhance handling. These alignment settings and soft tire compounds result in tires wearing out earlier than anticipated. This is a compromise made to have a car with exceptional handling characteristics.
The MAP sensor contacts can shift at high RPM causing a hesitation. Replacing the MAP sensor will repair the problem.
Some S2000's can develop a problem with the transmission popping out of fourth gear. A new updated fourth and fifth gear assembly will repair the problem. The transmission will have to be removed and disassembled for this repair.