s2000Junky

I chalked mine up to my sensitive ears and determined it was a normal amount of noise for this car. Possible, it could be a little more pronounced then other trans i've had in the car, but its been operating/working fine and not getting worse. To the average person they likely wouldn't notice without me pointing it out and even then you have to really key in on it. There is definitely a point where the noise is giving way to an issue, the hard part is determining where that threshold is and articulating it without a good way to hear it. It has to be pretty severe to depict over a youtube vid.

But the symptoms you describe IF indeed coming from the trans, can only be one of two things. Either the throw out bearing or secondary shaft bearing/s in the trans.

LagunaPearlAP2

I have a question about "I have a whine in neutral/idle and revving as well and don't know what the issue is." does your sound increase with revving? My secondary output shaft bearings were toast and replaced with positive results, but the noise for my car was 100% speed dependent. In gear, out of gear, turning, in N with the engine off, the noise was always there, and built up with speed.

s2000Junky

Sounds like the rear diff or wheel bearing.

LagunaPearlAP2

I could tell it was not the diff or wheel bearing by lifting the center tunnel cover (arm rest and cupholder) and having my wife put her head near that area and listen. As well, the sound did not change when turning left or right, so I could tell it was not a wheel bearing, or a diff bearing outputting to the axle. When I changed my secondary output shaft bearings my noise was 100% resolved.