What's the voltage at the back of the alternator on the lug.

I agree, if you painted any where there is a ground that could be your issue.

If you have the same voltage at the back of the alternator (12.7 ish) run a jumper from the alt case to the battery negative terminal. If it's charging find the bad ground. If not, you got a bad alternator out of the box. Not uncommon at all.