I just bought an '05 GT, with 30,000 miles on it and I'm having the same problem. When I try to ease off the clutch, such as in traffic, at a drive through, etc. It will shudder badly. Mine also acts up more when its warmed up. I also get a rattling noise when releasing the clutch sometimes, even with the transmission in Neutral, and sometimes when I first start the engine. I took it to a dealership today, and had one of the techs ride with me, and I was unable to make it act up. He told me that I probably just wasn't revving it high enough, but I've owned several Mustangs, and one thing that I can't be accused of is driving like a granny
I tried to get the clutch to slip by downshifting hard on the freeway, and lugging it in too high a gear, and it seems to hold well, but warpage or glazed spots might explain why it only does it sometimes, and mainly when hot.
I have a warranty on the car, but if I'm going to replace the clutch, then I'll go with a better aftermarket one. I will soon start modding this now bone stock GT, and be looking at getting upwards of the 500HP range, so what would be a good choice for a replacement clutch/flywheel that will hold up for the long run?