I'm no expert but have done a lot of repairs and fixes on A-Body harnesses, especially 67-69 Cudas. This is something simple . My guess is that something is not connected properly (you said it yourself.. everything worked before you took it apart). Retrace the way you re-installed the harness and pay particular attention to the pink and yellow circuits. That's what controls the light circuit. I would re-install the door light switches get everything working, close the doors and wait for the lights to come on. Then, remove the fuses one by one until the lights go out. This is the circuit feeding the lights and the one to check carefully. Keep us posted.
