Battery shorting killed all power

A little late for suggestions/ lectures, but this is EXACTLY why you attach the neg/ ground cable LAST

What you describe makes no sense, unless it burned the post/ clamp connection. suggestion above is good. I often use a test lamp instead of a multimeter, as it is quicker and more forgiving. "Follow the cables. Ground the lamp to somewhere on the engine, and probe the alternator big stud where the black wire goes, the starter relay "big stud," the starter "big stud," and the battery POS post THE POST and then the battery clamp. All that should be "hot."

Try removing the clamps and re-clean the clamps and posts.