There are known convertible top issues.
Resources for the Repair and Maintenance of your 2006 Honda S2000
2006 Honda S2000
2006 Honda S2000 Problems
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.
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.
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.
There is an issue when the ignition switch is on for about four or more hours. The powertrain control module (PCM) can misinterpret serial data and cause the Check Engine Light to illuminate. A software update from Honda will repair this problem.
2006 Honda S2000 Recalls (Recent)
RepairPal Expert Overview:
The braking system uses an assist device called a brake booster. These vehicles use a brake booster that is operated by engine vacuum and in certain cases the booster may not be able to maintain a vacuum when the brake pedal is depressed. This will result in reduced braking assistance, requiring additional force on the brake pedal to stop the vehicle. Dealers will inspect the brake booster and replace it as necessary.
2006 Honda S2000 Questions and Answers
Will a convertible boot from a 2004 S2000 fit a 2006 S200