If you pay attention do you rest your foot on your clutch pedal at all when you drive? I did then I figured out your slightly putting pressure on the clutch which is moving the TOB and its wearing a spot in it therefore it starts to make noise. If it were me id replace the tranny im having the same issues my second gear grinds almost all the time now unless I push in the clutch and wait for the engine to slow a bit. so I am going to buy a new tranny around tax time.