It is very possible that the transmission is causing this grinding noise even while the Jeep is in neutral. You may need to isolate where the noise is coming from.
Leave the jeep on, open the hood and try to find where the noise is coming from. Depending on where your noise is coming from that should be the problem
It looks like you have blow your third gear. Get a new transition and engage the clutch while shifting gears. Not engaging clutch will damage the gears.
If you are having a grinding problem on your Jeep you should change the brake pads. If you change these then you should not have any more problems after this.