Clicking and gearboxes = not good. Sometimes it's as simple as a grain of dirt in the gears, but you stating "stops moving all together" is a binding issue I believe.
I run on a track with lots of little stones on it, and from time to time I get one stuck between the arms and outdrive cups...causing one side of the transmission to lock up, or the stone comes along for the ride making a "clicking" noise on the tranny outdrive cup's slot for the dog bone.
Without having the truck in front of me, I'd would tell you to work from the outside in. Taking off the motor and turn the tires by hand to see if you can isolate the "clicking" noise. Dogbones staying in the drive cups? Do you feel any binding?
I'd take off the gearbox altogether and turn the diff outdrive cups by hand to get a better feel/sense of the noise taking place. I couldn't let anything go unchecked, now that I had the gearbox off the chassis. Look inside for any gears that might have broke or chip a small piece off one of the teeth. Get to know the tranny; being careful to not let pieces jump off your workspace as one disassembles; inspects, and reassembles all the little pieces/gears that make up the tranny.
Last edited by RustyUs; 08-11-2015 at 09:15 AM.