The only time the pilot bushing/bearing is used is when the clutch is engaged. When the clutch is out, the input shaft is spinning at the same speed as the flywheel. Not only that, but the input shaft is being is being held in place by the splines of the clutch disk, so the pilot bushing shouldn't be causing any issues. I wouldn't say it can't cause any problems, you never know. But when the clutch is out the clutch plate is being held in place by the pressure plate and the whole smash turns at the same time.
So, if its making the SAME noise with the clutch in or out, the chances of it being the pilot bushing are pretty minimal.
I'd put my money on something hitting the inspection plate or dust cover, or maybe even the starter gear contacting the flywheel. The starter often requires shimming to get the gear to clear the flywheel. Did you use the correct flywheel and pressure plate bolts? Are they still torqued to spec?
