When i turn on the motor, my tranny makes a loud "whirring" noise. After pressing in the clutch, noise disappears but when I start driving from 1st to 5th gear, the noise is back. Even while I'm rollin in neutral or with teh clutch depressed the noise is still there.Could the mainshaft bearings be shot?

 

could sound like your cluths is broken ( loss springs) !?! had the same problem..

 

the clutch, throw out bearing and flywheel are all new

 

My GS-R tranny has a bad imput shaft bering, the sound goes away when I press the clutch in.

 

if it does it in neutral
it aint the transmission.
ho long has it been doing this? sounds like a bad disc or worse...

 

the main shaft is still spinning when in neutral.

 

My car makes this noise too. I just put in a new cm stage one clutch and light weight flywheel, the flywheel had a bearing in the center that the stock one did not. I think this is an alignment bearing, Where is the imput shaft bearing?

 

but with the clutch engaged would it still spin? (shed some light)

 

Sounds like a thow out bearing to me.. well,the first part of the post at least..
These bearings will make noise when the clutch pedal is released... if your clutch has manual linkage then you can SOMETIMES remedy the noise by pulling back on the shift linkage boot and spray lubricant in the trans housing hoping it will get to the bearing..