If you're looking at '05+ models, you should consider the '04 as well (they are identical). To answer your questions:
1) Test drive/examination:
- When the engine is idling, listen for any loud tapping. The timing chain tensioner goes bad on a lot of S2000s. Luckily it's a cheap and easy fix (~$125 for the part).
- The transmission should shift smoothly, except for very slight notchiness when it's cold. If the 1-2 shift is difficult, look for another car.
- Check the soft top for any signs of wear or holes, ESPECIALLY in the area above the passenger's head, near the window. One of the support beams tends to rub this part of the top, eventually causing a tear. I had to get the entire top replaced under warranty.
- On the passenger side, the seam where the rear bumper meets the quarter panel (near the taillight) tends to misaligned from the factory. This doesn't indicate an accident or bodywork.
- Speaking of bodywork, do the usual inspection to make sure the car hasn't been in accident. I'd also check the top of the front fenders for dings, since those are hard to remove.
2) The tonneau cover is included with the car. Doesn't cost extra. With that said, it's pretty difficult to use and it takes up your trunk space when it's not on the car. You can find used ones for under $50 easily.
3) Just to give you an idea, I sold my '05 with 30K miles for less than $20K. For $22K, you can probably get an '06 or even an '07 with under 40K miles. With an '06+, you'll also get traction control, drive by wire throttle, a thermometer, solid headrests, different wheels, and some small interior updates.
The S2000 is an amazingly reliable car, considering how it's meant to be driven. A lot of people bought them as weekend toys, so you should be able to find a clean, low mileage example. Maintenance wise, they're extremely simple cars. The 15K and 30K mile services literally consist of: oil change, air filter, in-cabin filter, transmission fluid, and differential fluid. That's it. The car doesn't need a valve adjustment until 100K miles (you can do it sooner if the valves are noisy).
Hope this helps, feel free to ask anything else.
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