Adrenaline,
With the bike in neutral, all of the clutch and the transmission mainshaft are spinning. When you pull in the clutch, the clutch basket is still spinning, but the innner hub and trans mainshaft stop. When you install your new basket, replace the needle and sleeve no matter what they look or feel like. Honda has no specs for these parts, so unless they are measured against new parts, it will be hard to tell if worn. The noise could also be coming from the two mainshaft bearings. Some minor changes in noise is normal when engaging and disengaging the clutch. I hope you aren't chasing ghosts.