I have exactly the same issues with my 6 speed..
No idea where the clutch noise is but have had the box dropped when I got the SYE done and they couldn't see anything wrong
Same issue with the whine but most noticeable in 4th.
Previous owner had the box re-build (I think because of the popping out of gear issue.. worn fork) and it wouldn't surprise me if they didn't put it back together properly. When I had the SYE installed the ouput shaft looked like it had been attacked with a hammer. Invoice showed bearings and syncros replaced but the idiots filled it with ATF instead of the proper oil so it crunched every gear change. replaced with royal purple and now only crunches if I shift from 1st to 2nd quick or when cold. He paid over $8K for the rebuild too
I think you can get a new one imported from the US for that price
Would prefer a 5 speed and if it craps itself will look at this option. Not sure how easy it would be to retrofit but NV3550 from what I understand is a stronger, more reliable box