I have an occasional "chink" on engaging 3rd gear when cold, and occasional slight notchiness in all the other gears, especially second. It's much less common on downshifts. So many owners have noted this that I'd say it's completely normal. This is a very sporty gearbox after all, and the linkage is direct. I've read that the dual and triple cone synchronisers used in the S2000 are intrinsically notchy. Don't worry, your gears aren't grinding. Just enjoy the mechanical purity of the thing.

 

I also got my s2k at Lute Riley and I had 25 miles on it with no problems. Everyone there was really nice and professional, I doubt they abused your car.