HERE is how you troubleshoot this kind of thing
Get yourself an old headlight that works, or a stop/ tail lamp and socket
Wire the two pigtails of the lamp socket together as this causes a stop/ tail lamp to become one larger lamp
Connect the shell to a ground in the body/ engine, and connect the pigtails to the battery negative post with the normal ground cable disconnected. In other words the lamp is in series from the battery neg post to ground
Now, a short will simply cause the lamp to light, which does two things. As you disconnect various circuits, and the lamp goes out, you know you have found the area of the problem
Second, the lamp protects pretty much the entire harness as not enough current goes through the lamp to cause the short to do any damage
ALSO SUSPECT that the alternator itself may be shorted