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So I've got a strange whine coming from the trans on 1st and 2nd. It increases with the speed of the trans and stops if I push in the clutch pedal. All fluids are at the right levels and there's nothing floating in the fluid. Also, the sound doesn't always occur right off the bat either, just to complicate things. Any ideas?

 
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could be the throw out bearing is so get ready for the ride of your life. Most of us have had either syncro's or throwout bearing issues.

 
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Yea its deff a syncro or throwout bearing.. my 99 did this..

 
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if not those, it could be an alternator whine (but only if you just installed some new speakers/sound system)

 
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if it stops when you push in the clutch, it's your input shaft bearing. ive done a few on these cars, they're not fun.

 
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mine did it with the clutch out, and it was the input shaft skip.

 
Rep Power: 330

^when they get really bad they do it all the time. The OP says it which leads me to believe the input shaft bearing isnt totally mashed out yet. give it time and it'll start to get really annoying.