If I have clicking in a 3 diff car (and it doesn't click while all wheels are in the air) I hold the front wheels on the ground with the rears in the air and give it some throttle for a few seconds (if it's cogging don't keep pushing it). That will put load on the center diff and the front diff (the amount of load will depend on your center diff oil)
If there is clicking then it will be the center or the front.
Then do the opposite with the rears on the ground and the fronts in the air.
If it is clicking then it is the center or the rear.
If it clicked both times it's most likely center diff related. When it's the center diff spider gears it will often be jerky as well, because when they slip (and click) it swap between diff action, to locked diff, to no power fairly quickly.
If it only clicked when the rears are on the ground then it's likely to be in the rear.
If it only clicked when the fronts were on the ground then it's likely to be in the front.
If it didn't click at all, but still clicks while driving then your center diff probably doesn't have thick enough oil to cause enough load to find the click.
I think it was the pinon- the teeth on it were rounded. which leads me to beleive that it just wore out...
Did you rebuild the diff with new bearings? If the teeth in the diff were worn off, they would push past each other and wear out the bearings. When you put new gears in with those old bearings, they will slip past each other much easier.