i rebuilt a 98 trx450es.  it was beat, petty much replaced everything but that one way bearing, looks like number 7a.  doesn't make noise when running but when you kill the engine it will sorta knock.  the bearing is gone and the engine also doesn't have compresion braking will free wheel down a hill.  but it runs and drives good, and the owner didn't want to drop another $80 for a bearing.  maybe that bearing beaning **** is the noise your hearing.  the clutch hub number 1 will rock around.   
just read your last post, #1 should spin free when all together, maybe that was contributing to the noise you heard