Is the noise actually coming from the engine or from the transmission? Hearing a rattle from the transmission is "normal" (at least on a 97 GTS). The first time I heard it I took my new car back to the dealer. I have heard that this problem could be fixed if the idle were turned higher. The Viper uses the same transmission as the Vette, but the Vette has a higher idle so you don't hear the rattle.
The real fix though is to put a good exhaust system on the car. I have a Borla system and I do good to hear the stereo, let alone rattles!