Tek, me and you always seem to end up with the same problems on our skylines lol. I'm having this exact same problem. Clutch was just replaced with a Jim Berry made clutch, hd organic type with 2100 clamp load. Noises occur whilst accelerating before about 2,500 to 3000rpm in all gears, except for maybe 5th?? Not sure about 5th.
My fly-wheel was machined when they replaced the clutch. Throw-out bearing was replaced. This was only a week ago. I replaced my gearbox oil about 2 months ago with Motul 300. Wtf is this noise lol. It's not cool hey.... fix one thing, another breaks.. Still love my skyline, but man.....
EDIT - Gearbox feels completely fine to drive, no gear changing problems etc that would suggest synchros??? Please help.