Slightly long reply to an old thread, but bear with me:
I had the exact same noise (and occasional shudder/stall), mostly when it was cold, mostly right when it started, but sometimes when coming to a stop as well. I had just been putting up with it literally for two or three years.
Two weeks ago while on vacation in New Jersey, it started getting pretty difficult to get in and out of gear, so I dropped the car off at Kindle Ford in Cape May Courthouse
so they could look at/replace the clutch.
Turns out the transmission has a steel housing, but apparently there is an aluminum cone-shaped piece that is press-fit into the front, behind the clutch and pressure plate. Somewhere down the line, that cone started to work itself out of the main housing and was actually rubbing up against the back of the clutch/pressure plate assembly, wearing it out prematurely (and making the nasty metal shrieking noise).
They were going to replace the aluminum piece but they couldn't get the part in time for me to head back to MA, so they worked it back into place (I assume with some fancy rubber mallet work). Their logic was if it took 100k miles or so to work itself out of there, I would be good to go for at least a little while. A new clutch, a new shift fork (see what happens when you shift like a maniac with a worn clutch? Pay attention kids!), and some labor, and I was good to go (minus about $865).
I'll bet that's what is wrong with MrKrinkle and dpizzi's Stangs...