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Transmission clunk

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Hey guys, I see this is slightly covered in the transmission pole thread but I figured I would ask more specifically about the issue I am currently experiencing and any input from others to see what the cure/cause was. Since new the transmission has had a slight clunk when shifting into 2nd, 3rd and 4th when cold. I have since changed to an MGW shifter which I know wasn't the solution but I figured I would try as I wanted to install the shifter anyway. I am now at the point where I have finally taken it into the dealership to have them look at this for fear of doing damage to the internals on this transmission. They're going to look at it tomorrow as they're busy today and with the new snow fall I am hoping this can be remedied in short order so that the car can go into hibernation for the winter. I suppose some more points to note are that once the transmission has warmed up, the car shifts nice, when the temperature of the transmission is cold (|hasn't been driven in a few hours/days) is when the problem arises. I would appreciate any input from others who have had and/or cured this problem as to what you changed. I am thinking I will order the Ford Racing stainless steel clutch line to see if this improves matters while they have things taken apart. Again any input is appreciated, thanks guys.
I wouldn't let the dealer monkeys drive your car around all day to lunch and shiznit just to tell you there's nothing wrong.

My GT did this and my Boss does it. Comes with the territory.
I went with the production service manager for a ride, he seems to have an idea, sounds like he will be the last to drive. I also have a friend that works at the dealership that will keep an eye on things for, unfortunately, he's not the manual transmission guy at the shop.

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