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 2006 Honda S2000 problems
On certain models the PCM misinterprets data from the coolant sensor and causes the Check Engine light (MIL) to illuminate. A software update from Honda will repair this problem.
There are known convertible top issues.