Somethings bad?

There are other sources for harnesses other then Year one,they are usually higher on there product.You need to go through your electrical system to see if you have another problem,with this episode you have had im sure your going to have other problems now,wires melted together are never good.The ballist you dont need with the Msd and you should have the later model voltage regulator(flat,square with a triangle plug)Go to mad electrical on the net,that will show how to get past the amp meter.

Hot battery is overcharging or a direct short,with what you have going on could be either or,(back to the melted wiring).