I decided to grease the shaft up, but it didn't solve the squeak noise. It appears the noise is coming from the master cylinder. Did anyone have the same issue? I'm not very familiar with the inside of the master cylinder - can one grease up the inside without leaking the fluid?
Hisashi
Greasing the shaft is unlikely to solve this squeak I fear. The pedal rod simply pushes the piston inside the clutch master cylinder, and it returns under spring pressure (with some assistance from the pressure plate returning to its uncompressed state). Now if there is a squeak when you pressure pedal down, that is either coming from the pedal pivot or rod pivot, or it is the clutch master cylinder piston rubbing the inside of the bore.
Removing the clutch master cylinder from the bulkhead will do nothing, and there is nothing you can lubricate to stop any squeak. A squeak is usually caused by two parts rubbing one another, and since the only item moving and therefore likely to be rubbing, is the piston. To get at that, you would need to strip the master cylinder and therefore you would need to drain the clutch fluid first.
Roy