Bobtam

I at my wits end. My 03 Z06 Has a noise coming from somewhere in the drive train. Everything works great cold. Once its warmed up every once in a while it becomes difficult to shift into second and third. Effort is hard and it makes a whirring noise when shifting into gear. Sometime this noise has continued even when I shift into neutral and then it just goes away. Not as course as if it were syncros not a grinding but a scraping noise. It will drive great for a while then happen again.
The clutch is a Monster Stage two and it seems to work fine. Installed last year. New fluids did not help bled the clutch no help. Adjusted the shifter linkage no help. Most of the time you cannot notice any problems and then it happens again. Had the skip shift deleted with a tune but that was a couple of years ago. Could something be happening with the shift solonoids? Also caught reverse going into 5th very quickly pulled it out. I thought that there was a reverse lockout.
Anybody have any Ideas?