If you found a piece of gear tooth when you drained the transmission oil then you have identified the problem and yes using it in low range with a broken tooth will do more damage.
You can use the old wooden broom handle trick to get a general location of where the sound is actually coming from.
I can't help you with yours, but my 3000 diesel makes no noise in low or high range. So you definitely got something going on. I would really try and find where that piece of tooth or metal came from.
Well once you get it all straightened out I hope you enjoy it as much as I like my 3000.
I got one more fall agricultural fair to attend with it, then I will also be pulling off the lift cover to change my filter and put new gasket and o-rings as my rear remote valve is leaking at the base.