Assuming the clutch is properly adjusted, try these tidbits:
http://blog.latemodelrestoration.com/common-mustang-clutch-problems-causes-solutions/
From SVT Forums:
Throw Out Bearing Adjustment
Hi guys, I put a new Ram clutch (with TOB included) clutch in a few months ago and had no clue how to adjust the TOB, so I tried to do what I could from what I found from info online.
Anyways, I adjusted the clutch as loose as possible but with enough slack so that the cable has no free play, and as little pressure on the pressure plate fingers as possible.
Now I'm starting to get a chirp that is RPM dependent that happens when the clutch is in relaxed state, in gear while driving. I have 2k miles on the new TOB. If I lightly touch the clutch pedal, maybe 2-4lbs of pressure, the noise goes away. I'm afraid to tighten the clutch up that much though because they say you will kill your clutch fast if you ride it (leave your foot on the pedal) and tightening up the clutch even more is like doing the same thing.
I have no clue what to do, results for adjusting a TOB come up as you have to leave a clearance between them and the fingers, but I don't know how that is possible with a cable clutch unless I rig up some sort of spring or magnet system.
A: I just put a little preload on mine, so that the noise is minimal. I'm sure it's not the optimal solution, but hey.. it works. My clutch is about 3 yrs old and has about.. i dunno 45000 miles on on. It's getting pretty bad as of lately, can feel it slipping like hell in 5th if I try to gun it on the hwy, and even 3rd and 4th if I downshift and punch it. So for me since the clutch is goin bad I have no problems preloading for the sake of ride comfort. It used to annoy me so much I could barely stand it... Now.. no more birds under the car.
A2: The TOB is not supposed to ride on the PP fingers all the time. This is what I did - I put a long spring (went to Lowe's until I found one the right length; I tried several) that attaches at the clutch fork end and to a bracket I made attaching to something else that had a nut straight back from the attachment point - maybe the tranny but I forget exactly where now). Then, I adjusted my firewall adjuster until there was like an inch free play at the top of the clutch pedal, which insured that my TOB was away from the PP fingers. I've got 57,000 miles on it and the stock TOB is quiet all day long. Someone makes a spring kit for this application but I forget who it is right now. And, yes, the stock Ford TOB is the only way to go.
I think you are going to have to pull that tranny again and replace it - sooner or later.
