Well, it doesnt have to be tranny if it is only in gear. When in gear, the engine is under more load, which will make a bottom end noise worse. It is hard to determine without driving and listening to the car, which makes it hard to e-troubleshoot it

 

My problem was with the supercharger itself. When in gear it was making a noise .... turned out to not be the trans ...but the shaft.

 

here is my video i have some sort of ticking so too. i have injen cai,spipe,magnaflow catback, and ap crank pulley.

 

does it get louder when you hit the gas? ...thats what you needed a video of