if you spilled paint into the alternator then you probably now have a short to ground through that paint. normally there are diodes in the alt to stop a back flow of power, so if the paint shorted the diode, then it makes sense you have a melted wire. disconnect the wire to the alt and see if the short goes away. or just take the alt out and have it tested. you should do that regardless. did you have a problem before the paint stage? or was it after the paint spillage episode?
make sure to check the wiring for burn/melt through. otherwise you will have one circuit melted into other circuits in the harness and cause all kinds of problems.