Have a aftermarket 5 speed in a 4 speed case . Noticed some winding noise so I pulled it apart I did notice some issues with the clutch 1 stud was loose and last fiber plate was gummed up also roller bearings on hub seem a little loose but what I'm really concerned with is this I have the back wheel off the ground and it spins freely in neutral but when I turn the main shaft there's some clanky noise from trans and the rear wheel moves just a tiny bit in either direction. thought there were some clutch problems ! Down the road it shifts fine in every gear and hits neutral when you want it!

 

also makes more winding noise when clutch is pulled in !

 

Noises are almost impossible to diagnose over the internet! You mention 'winding noise', which might be a bearing, if it is continuous, however gears also whine when everything is OK.

How long have you had this bike and have things changed recently?