I know from hard experience that if you hook up one of the Actron lights "backwards" it will kill the car immediately. The instructions for these lights say that black is ground and that the red should be at "battery positive" - which can be any hot power source. They usually warn not to hook up to the coil LT side, but not always.
I know what I'd be doing right now, but it's not my car. /ubbthreads/images/graemlins/nonono.gif
As long as you've absolutely 100% confirmed that it's currently - no pun intended - battery positive-to-ground, it sounds like things should be swapped around. Before doing that, though, I'd want to run down every important circuit - instruments, lights, and charging system - to make sure what went where. Use a multi-tester and double-check everything against the diagrams from Advance Auto Wire, including color coding. Very time-consuming (again, based on experience) but necessary, methinks.
Take your time, be methodical and patient, and have extra fuses on hand.
Rick