Well i just got done doing my 5 speed swap found a leak and while fixing the issue the tapping arose, i took it to the tranny shop and i was told thats what it was. Now someone else correct me if im wrong but the reason it does not make the noise with the clutch in is because the input shaft is not spinning, or doesn't have a load on it. I just got the car back, and no more tapping at all, Ive come to the conclusion that although bulletproof for the most part things break, and its something stupid, in my case was the bearings. Cost me around 500 bucks to get it fixed. Take it to a tranny shop see what they say.