I have both a NA1 NSX and an AP2 (2005) S2000. I have never tracked my NSX (nor do I plan to), but have taken my stock S2000 to a HPDE class. I've taken other cars before, but the S was simply amazing. I achieved faster laps than ever before without ever straining or abusing the car. So if you plan to track your next car, you can't go wrong with the S.
Here are my thoughts on the S2000 from a NSX owner.
1) Cost...the S2000 is significantly cheaper than the NSX to own and maintain. Some key maintenance issues have been addressed, thus ownership cost is much less.
a) No timing belt!! The S2000 has a chain which should be good for the life of the engine.
b) Advanced ABS. The ABS unit is similar to the newer NSX's so you don't have that solenoid issue some of the early NSX suffer from. No secondary resivoir to deal with either.
c) Clutch is far cheaper in parts and labor.
d) Parts in general are cheaper.
2) Mods...haven't done any on either of my cars, but I believe that there are more for the S.
3) Handling...The earlier S2000 (pre-2004) had a more edgy handling behaviour while those manufactured after 2004 are more subdued. I'll add a few comments here.
a) In 2006, Honda went to a drive by wire system that included stability control and a different ECU. I believe the later allows for some different engine mods as well.
b) You may also notice that in 2004, all S2000's went to 17" rims. Not sure exactly if this improved performance or just looks.
c) Steering feel and rack were changed on the AP2 except for the CR version which got the older AP1 steering rack (hence its different feel).
4)Noisy...compared to the NSX, the S2000 is awefully noisy (mostly due to its soft top). The AP2's have less drone compared to the AP1's and are more liveable.
5)Weak stereo...Now I know you are looking for a track car, but wasn't sure if you were going to drive this vehicle to the track or not. Just thought I would mention it.
Now for some S2000 nuances, that you may or may not know.
1) The rear glass window was added in 2003 (I believe). I prefer this cause it doesn't fog up with age.
2) The AP2's (2004 & older), have different synchro's that from what some have said make the tranny shift smoother. My boss who had a 2001 S2000 thought mine was quite a bit smoother than his. I believe this maybe a personal perception.
3) The AP2's have a clutch delay valve that does result in greater wear on the clutch versus the rear differential. Some people hate this and modify their unit to remove it. Results vary.
4) In 2006, when they switched to the drive-by-wire, there was a software update to address an issue with the feel of the drive-by-wire. If you find a 2006 and it doesn't feel "right", it may just be a software update fix.
Overall, the S2000 has a low cost of ownership and a big fun factor. I don't believe you can go wrong with acquiring a S2000. Personally, I would get an AP2 if you plan on having it do daily driving duties; however, if you are going to relegate the car to exclusive track duties the AP1's might be a better choice for you.