i have an 05 gt 5 speed that sometimes gets a "vibration" in first and second at 2000 and 3000 rpms. it only last for a 1/2 second and doesnt do it all the time. im all stock except for magnapack cat back and i noticed the noise before the install.
good luck withnthat one. the dealer will most likely point to the exhaust, even if you did hear it before the exhaust was installed. most dont like to track down things like this.
It's fairly normal to hear noises from these trannys due to the shifter being mounted to the body. Mine makes some noises and then it will be quiet the next time I drive it.