If the cases are ok, then just change the gears, but do both.
The crown wheel teeth may look fine to the naked eye, but they will have a wear pattern in them.
If you reuse the crown wheel, you'll have trouble getting a good tooth mesh.
Now's your chance to put things right.
I'd reuse the factory shims in their original location to start with and adjust from there.
You mentioned about replacing the bearings before, I'm assuming you've replaced the pinions needle bearing?
If you had and then run it with the old worn pinion, then that needle bearing is probably damaged, so I'd replace it again.
You stated that you have a workshop manual, so just simply follow the procedure and you should be fine.
One last thing, think clean, clean, clean when you do the work.
I am a little curious as to the low km's for the diff. My 2013 Outty has almost 20,000km and no sign of diff failure at this stage.
Of coarse, now that I've said that.........