Jump start gone wrong

So my wife tried to jump the car. She obviously reversed the clamps on the dead car. I replaced the battery and now when you turn the key to on nothing happens at all and does not crank or click when the key is turned over. However, when you connect the jumper cables to the new battery and turn the key on the interior lights and exterior lights come on but no radio or door alarms. So I crossed the main fused that is bolted down above the under hood fuse box with a pair of players and the door alarms come on. Also when the jumper cables are connected the car will turn over a few times slowly and then start clicking rapidly. Could it just be the main fuse or did she rally mess something up? I have heard the main fuse is supposed to prevent damage the the ECU and other factory electric components.