Keep pulling fuses one at a time until it stops, then you will know what circuit is powering the fan. If they replaced the wiring harness, you might want to get a wiring diagram and trace down the wires back from the fan lead. It sure sounds as if the ground for the blower motor is coming through the pin switch circuit for the interior lights and not through the blower motor circuit. I am not absolutely sure they are the same, but the Plymouth diagrams below should give you a start.
I like to highlight the circuit on the digram with the appropriately colored marker, and then follow it through in real life. I think you will find an orange wire connected into the circuit inappropriately. Good Luck, these things can take some time, but they are pretty simple circuits.