Seems there has been an on going issue with gertag manual transmissions made in China. I took mine to a dealership with around 1000 miles on it. They had me test drive another got on the lot with a manual transmission, and it clunked as well. The issue has been documented

http://www.edmunds.com/ford/mustang/...unk-sound.html

Love my car, but would love it more if the transmission did not clunk. Interested to know what you think?

 

I've noticed this in mine as well. It's not overly annoying. I have had several manual transmissions in various cars over the last twenty years. I've had spongy shifting, grinding shifting, you name it. My new GT is easily the most solid shifting, but most "thunk"ing one I have had. Truthfully it doesn't really bother me. If it changes for the worse substantially, I'll make a visit to my service bay. Beyond that, it's the most fun I've ever had in a car.