My 2004 3.8 was doing the same thing after a transmission install. It would squeak when the pedal was not depressed, then when you would rest your foot on it, it would stop. Right before I was about ready to tear the transmission out and throw it in a deep dark hole, I found the solution. I pulled the cap off of the clutch cable housing and disconnected the clutch cable, then I gave the fork that the cable connects to a pull so the throwout bearing rode a little bit differently in the mount, and my squeak stopped. Make sure you readjust your clutch by pulling up on the peddle afterwards.