2000 3.8L clutch squeels when engaged and disengaged

It's defintly your clutch, possibly throwout bearing. Replace it quick. On my 00 v6 mustang there would be a subtle squeaking sound you could hear I was idling and when you depress the clutch the squeaking went away. I thought it was the throw out bearing (It was) and since I wanted to try and get max miles out I let it go. The sound did get terribly worse and switched from going away when depressing the clutch to always there. I say this because you should replace it asap because mine ended up tearing up the input shaft. Was able to be sanded down but if it went farther woulda needed a new input shaft and thats not fun. As far as your flywheel did you check the forums, if not id sugguest you do a search because you can most likely find your fly wheel questions.

some tranny shops wont even turn it down they will just replace it. i know the one i go to does casue for them to have it turned down they have to send it out and then have it sent back and that takes like a day or two so they find it easier to just replace it.