03 Cobra has it and so does my 01 GT (but not as bad). Also, I've noticed that rapid shifting seems to help. But since I'm still breaking in the Cobra I am only shifting gingerly.
I do, but only if I'm not careful. Can shift "clunkless", 99% of the time. People just need to synchronize their shifts to what the driveline likes. My '98 Cobra was the same. With practice, clunkless. New driver, clunk-city.