Same noise here with lighter flywheel and ACT clutch. That's the price you pay to play.....
Mine also becomes noisier with increase trans temp. If I start the car at let it idle till the engine is warm the noise is not there, however if I drive and get the gearbox warm the noise appears. As far as I can tell it does have something to do with the gearbox oil viscosity changing with temperature. Tolerances in the box will also change with temp as well as the gearbox oil acting as a damper more so when cold (thicker) then hot (thinner).
Any sort of change in rotating mass will cause a change in the damping characteristics of the drivetrain. It seems that the lighter flywheel has brought the gearbox noise to an audible frequency that is perceived as extra NVH. The noise I hear (frequency dependent) will most certainly be impacted by temperature, load, speed, and rotating mass (dampening coefficient).
I am just happy that I was finally able to use my $200 vibrations textbook from university for something useful..... to allow me to stop worrying about my trans