Im gonna say pilot bearing. I had the same problem; started about 2wks tops after I bought my GT. Whenever I came to a stop and slipped in neutral and let the clutch out, it would start making a slight chirping sound. The noise became more frequent and louder the longer it went.
After I knew what it was, I ordered the pilot bearing, T/O bearing, clutch disc and pressure plate just to replace everything while the tranny was out. Turned out that the bearing was chipped on the inner diameter. The whole job took about 4hrs with a lift and air tools.
I have a rattle if my car uis iling and my foot is not on the cluth I will here a ratlle. As soon as I put a little pressure on the cluth it goes away.
Most stangs have adjustable clutches, just pull up on the pedel with you foot. But that does not fix my problem, but my rattle is just minor not anything major.
you have a while on it.. trust me.. mine's been making noises for months.. i'm workin on gettin it replaced soon tho.. i wouldnt sweat it too bad, but you'll know when it's about to crap out.. loud noises when you press the pedal in and when it's out..
My 99 has chirped on and off pretty much since I've had it with 100k on the clutch now and still going. It used to be bad in the summer, but not as bad anymore for some reason. In fact I rarely hear it now. Push in the pedal at all and it stops. Just a chirping noise, though, no clicking. Just FYI.
My Gt had a similiar sound that ended up being the TOB. Run a search on it.. I remember seeing a post a long time ago where a lube was used (I think white lithium but don't quote me on that) and it was a near-permanent fix. I personally got a new clutch under warranty.
Mine has been doing it since last year in the Summer. If the car is in the driveway or running the sucker is so loud you can hear ir 50 feet away. Ive probably put 25k on it since it started making the noice. I figure its the TOB or possibly the springs on the clutch plate are or arent releasing enough or too much. also thought the plate might have warped and might be tapping, either way not going to do anything until required, which was advice from 2 mechanic's