Gearbox Noise?
 

https://youtu.be/uDuHpS9rick

A slow clicking noise coming from my gearbox.

When I apply the clutch it goes away.

Help??

Suggest you search for a tool called "Engine Ear". Use it to located exact source of noise.Best with an assistant who keeps moving the 'ear' around while you use the headset.
Check motor(engine is Aussie) mount- common failure
Remove panels under engine to do the inspection.
Plan on spending several hours on this.
Need ramps to do a competent job.

It's definitely coming from the gearbox.

In neutral and in gear?

Yep but goes away when I apply the clutch.

Let me guess. It works perfectly fine and you hear it at idle and in lower gears. Probably a bearing.

I believe I get this on my six speed when it's sitting in neutral at idle. I couldnt begin to guess what it is. It seems that once the trans. is loaded it disappears. On shutdown the rattle freq speeds up considerably as the engine trans mass vibrates through unbalanced harmonics....then dies with the engine.

My sound is much more intermittent and quiet than what I hear in your clip.

It feels like undue axial play in the trans while unloaded / in neutral

I hope nothing critical is fretting while sitting neutral....

Did you fix or replace the trans you chipped a gear in?