When you say the harness burned up do you mean the insulation melted? Look to see which of the burned wires was the hottest by looking for discolored copper. That wire is likely the circuit with the short. The short must be found and the fuse protection verified.
Does this happen with ignition ON? Or ignition OFF? Or engine running?
This is a process of elimination.
Disconnect the battery positive terminal. Connect a test lamp between the battery terminal and the battery cable.
Remove all the fuses and turn off all accessories. If light is not lit proceed to replace the fuses 1 at a time until the test light lights. Check out the circuit that causes the light to light. It could be the normal load or a short.
If light is lit with all fuses removed the problem is a short somewhere in the main red wires that feed the fuse block, starter and alternator. This main red wires should be protected by a fuse link that comes from the battery.
Is it possible that this fuse link has been by-passed?
Let us know what you find.