My 06 GT clunks only from 1st to 2nd on low speeds , wether warm or cold .
I avoid the clunk waiting about 1 second before inserting the 2nd gear , clutch down .
it's a feature of the 5 speed being very notchy combined with a heavy rotating assembly and a two piece driveshaft. I hear lots of noise will go away if you swap the driveshaft for a lighter one piece unit and lighten up the flywheel.
Actually, this is not true. The oem driveshaft is designed to conceal noise. I have the one piece, lighter driveshaft, and I still have the "clunk." However, it's not a major issue for me, and I consider it the "nature of the beast."