I had an issue where I used some slightly long screws to mount the spacer used when you run the shocks on the rear. The screws pushed the gear box moulding into the top the of the diff. It only made a noise once remounted and tightened up so wasn't obvious.
I would check the bearings and make sure every thing spins freely with the other half of the gear box off, then put the gearbox together and check gain. If no issues I would mount it back in the car and check again by hand and finally with the motor.
Obviously make sure the idlers etc are in good condition and you have no dirt in the or debris in the gear box.
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