does a 2001 mitsubishi eclipse have a pilot bearing in the clutch

did you replace the throught out bearing when you changed the clutch. that might fix the grinding noise. the pilot bearing is in the crank shaft, doubt its the problem

hydraulic clutch,did you bleed all the air out of system.

it wont be the throwout bearing. he said the noise stops when he pushes the clutch pedal, if it were the throwout bearing, it would make noise when he pushes the pedal. im pretty sure these vehicles actually dont have a pilot bearing, but it could still be the input shaft bearing being worn out.... does it make the grinding noise in all gears once you let the pedal out all the way or just in neutral?

Yes they do have a pilot bearing... but it might just be the breaking-in of your clutch wait a few weeks and see what happens.