So it only makes it when the engine is powering the drive train.
Or does it make it when you rev it?
I think you said it doesn't.
I'd look at all hubs, both propshafts, including taking them both off as you can't feel it when on the vehicle. This is how i knew i had to replace my front one as the slight play in the cardan joint was only obvious off the car.
Then you are down to the gearbox, clutch etc etc.
BUT it could be something to do with the engine bearers as when the engine is under load, it'll compress one side and stretch the other, which could just make metal to metal contact somewhere.