Noises problem
1994 Ford Mustang V8 Two Wheel Drive Manual 174000 miles

I just installed new clutch, DID NOT resurface flywheel, or replace pilot bearing. There is a chirping noise while in neutral that will stop when I push clutch down some, also kind of a shaking in shifter. I just had transmission fluid put in, so its not low, and guy told me it was flywheel without even looking at it, but could this be right, or maybe an input shaft bearing?

Many thanks