Hey guys, so yesterday this problem presented itself.

I've got an ACT HD Pressure Plate (used, probably ~20k miles on it), OEM clutch (brand new) and ACT Prolite flywheel (brand new). The throwout bearing had ~1k miles on it, but it was reused anyways. The original clutch fork was used that was in the car (~80k miles) every thing else was replaced when the clutch was done.

Anyways, the "below the shifter" area is making a whirring noise when cruising, the higher the rpm, the louder / more prominent the noise is. It is louder with the A/C on, and it goes away when I disengage the clutch (push the clutch pedal in). Upon acceleration it also makes a faint high pitched whining noise (think roots type SC, only not nearly as awesome). I've got about 5k miles on the set up since it was installed with the parts mentioned above.
More information, I've actually started having vibration at high speeds from an unbalanced driveshaft I haven't managed to fix just yet. (It's aftermarket). Would prolonged vibration from the driveshaft cause a problem with the output shaft?

Heres some links to videos trying to show the noise.

Cruising:
Noise starts at ~6 seconds in. Try to differentiate between the exhaust noise and the clutch noise (higher bitched grindy sound)
http://vid37.photobucket.com/albums/...psanhvb38r.mp4

Sitting at idle: I'm pushing the clutch in to demonstrate how the noise goes away dependent on clutch engagement, here it just sounds like very prominent flywheel chatter.
http://vid37.photobucket.com/albums/...psyelbysjb.mp4

Will upload another better video as soon as it processes:

 

Throw-out bearing starting to go bad?

 

Thats my best guess so far

 

Its either that or the transmission. I have a similar noise/situation, but its pretty faint so i haven't started to freak out yet. In situations like this, you will find out what it is when it fails. You have a 50/50% chance you will spend more money trying to address the problem early then just waiting for it to fail and fix it then. You can just buy a new trans and TOB now and replace both just in case, not knowing if you just bought a trans for nothing, or replace the TOB only, then come to find you have to do the job again because its the transmission. See what im saying? Just drive it, get a AAA membership now if you don't currently have one, it more then pays for itself the first time you use it. $100 a year is it.

And yes, chances are more likely its the trans based on what your saying about the TOB only having 1k, and the unbalanced drive shaft.

 

New symptom: Moving the shifter into different gears sounds very hollow / clunky. Much more than your typical "click"

Does this give evidence that the culprit is in the transmission?