my 94 525i did the same thing when in neutral. I never did pull the gearbox but it never effected any shifting issues. It sounds to me like the throwout bearing. the throwout bearing should be smooth as silk when you spin it.
I would change the bearing and anything else that may be worn. Maybe change the friction plate while your in there.
The list starts here: Depo headlights w 8000k hid's,/CCFL's
, smoked tails, corners and BBS RC041's/042's, Vogtland junior cup kit.
Lightweight flywheel ,clutch and SSK are in.....