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When I puch the clutch in it makes a noise in the motor go away and when i let out it starts again. Its not loud but i can hear it. And the pedal is really squeky. Any way to fix these things.

 
Rep Power: 217

My pedal squeaks when it's about to rain or if it's humid outside. I tried greasing up the rod(yeah yeah), but that only helped for about a few days. The noise you're talking about might be the release/throwout bearing
Check here and see if the symptoms match up to what you're talking about.

 
Rep Power: 0

i have an 03 civic ex and im having the same problem ive replaced the pilot and throw out bearing and the noise never stopped the noise is most likely from the trany internals

 
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thanks guys ill look into the site you gave me and see if i can get it fixed.