pilot bushing could be bad, (or not even there, seen that happen after rebuilds)
flywheel could be jacked up
pressure plate could be jacked up
the clutch plate itself could be jacked up.
could be something really dumb like the fork got bent

gonna have to pull it part to figure it out.

And that is only if you are sure it is coming from the tranny/clutch area.
There are all kinds of things that could be making a chattery/clicking noise, especially after a rebuild.