wiring question

68 barracuda, stock wiring harness.... alternator has a black wire that goes into the factory harness plug in the firewall????

Yes

and that is the stock charging wire then?

Yes, I believe it is the 2nd wire down on the passenger side of the center lug.

so now that i have a toyota internally regulated alt. that runs to my batt. what do i do with that black wire? do i hook anything up to it?