Sounds like maybe z25 gear/shaft. if you remove the alternator and check that the shaft cannot be turned too easily, or remove clutch cover and check at that end. Or it could be a sprag clutch issue but I wouldn’t have thought there would be any noise.
Was the noise there during cranking, running or both and clutch in or out? when you put the z25 shaft bits together does it look complete? Probably easiest to pull clutch cover off and see if there is any obvious wrong in there. The neutral light switch is in the back lower of the gearbox section if something has got in there and wiped it out. I think I would pull the gearbox out and have a look(not as bad as it sounds) and you could give the sprag a once over while you are in there.
i Would only do that if I could guarantee it wouldn’t fire. Maybe pull the fuel pump fuse or the injection fuse but they may have other feeds that would stop the starter motor, or pull off the coil sticks.
As Rick says doesn’t sound right. Sorry to say pull it apart again and look at bearings. Check everything is in the correct place by looking at the exploded parts list. Does the alternator spin free by hand? Good luck
if the clutch is off how do you start the bike? If it just the clutch centre then it will still run crank cams etc, the z25 alternator and sprag but nothing else. Have you tried turning z25 by hand should be more resistance one way as starter and alternator will turn one way and just alternator the other.
It’s a puzzle. There are 2 spacer washers on the clutch shaft are they definitely the correct way around? Is there any signs of the oil pump, primary gear and z25 gears being out of line or interfering?