ok well i had this problem up until yesterday. i have just finished a manual conversion with a T5 gearbox (cable clutch). i installed a brand new exedy HD clutch yet when the car ran it made a really annoying rattling/sqeaking noise that went away when you lightly touch or move the clutch pedal/throwout fork i also found that by putting my foot behind the clutch pedal and lifting upwards slightly the noise would go away. now i sent the car to a mechanic who is a mate and i told him that i thought it was the throwout bearing that was making noise on the input shaft, instead my mate found out that it was the throwout fork itself that was rattling around and making a fuss because these little rubber dampeners between the fork and the bearing were missing, apparently this is reasonably common with T5's. anyway after installing a stronger spring and some rubber dampening things in there the noise has all but disappeared. have a look through the clutch hole into the bellhousing when the engine is running and if you see some inbalance in there then this is your problem. i hope this helps...
