The difference is in the ammeter wiring. The 65 uses a large wire that runs from one firewall plug to the other, with a loop for the induction-type ammeter. The gauge harness plug is a 7 pin affair for 65. In 1966, the design for the ammeter uses two separate lines, both from the gauge harness plug. Thus, both the underdash and engine gauge feed harness are different from 1965 and 1966. I believe that the headlight harness also changed due to some modifications in the connections to the alternator/starter solenoid/engine gauge feed cluster near the battery.
You either have to stick entirely with the 65 gauge wiring for everything forward of the tail-light or the 66 version, all driven by the dash cluster year.