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Sounds like you have a throw out bearing issue...

 

If you're talking about the rattle that you can feel through the floorboard and the shifter, I have it too in my '96. Not sure what it is, except it shouldn't be the throwout bearing because I recently replaced mine and it still does it.

 

Definately your throw-out bearing..That's the reason it stops when you push it in a 1/4in. your actually putting tension on it causing it to engage some..Not a real problem just an annoying noise..Make sure to have it replaced when you do your next clutch

 

I get a rattle when driving at certain speed when in gear, the rattle goes up through the shifter, I think its my u joints though.