Is it normal for the S2000 to have lot of interior noise, especially the transmission on a 6spd Manual?

oh yeah! The hardtop only makes it worse. If you look at your flooring you'll notice it is a lot like a jeep. Metal floor with a layer of 1/4 inch carpet. So much for sound deadening. it is the essence of the car though. That is why many people will ask you repeatedly if you really want it for your daily driver.

The ride is harsh, loud, and extremely pleasing to a car enthusiasts soul!