Sometimes when I'm engaging in gear (riding clutch) usually 1st or 2nd gear my tranny will make this strange noise.

It's not a high pitched sound. I had that on my old d-tranny which I read was the throwout bearing.

Any idea on what this could be? It sounds very simliar to when you just washed your car and you step on the brakes and they make that funny sound.

 

sounds like throwout bearing

 

Input shaft bearing