Same issue as me, let me guess..

Jun Flywheel + Exedy Clutch?

Here's something taken from the official Exedy website

"The drivability will be similar to a regular clutch, however drivers may experience increased pedal effort, slight shudder and increased cabin noise due to the performance characteristics of the clutch. All of our clutch discs have high capacity sprung centre dampers to reduce the drivetrain shock and impact."

Also if you troll around the internet a bit, a few forums also rants on about the JUN flywheel increasing noise within the cabin around the 2500 - 3000 RPM area under coasting conditions or light load within the same RPM range.

I would be interested to find a solution to this issue, maybe someone with a standard rebuilt clutch with the JUN flywheel could comment on this issue?

Other then that i would say the only other thing to do would be to get over the noise and drive it as it is...

ahh yes.. i've also been told it could be signs of the gearbox starting to die also.. but to me none of these noises were present with my stock running gear.. so it leaves me a little dubious about the whole situation regarding my gbox.