Ok. You're getting there.
If its a short as you suspect
By taking the connectors off (as you did the middle) you can narrow down the location. It sounds like you've checked to see if there was a reading between the connector and the alternator's output and there was none.
Do the same for the battery charge/supply wire.
Then check between one of the matching terminals on the bulkhead and ground.
-> If there is reading, then it must be inside.
-> If its open, check again with the ignition switch on 'RUN'. If its still open, then its one of the circuits that got disconnected when you removed the connectors.


The coil gets power from the ignition circuit.
During Start power from the starter switch goes directly to the coil.
When running power from the Run position of the switch goes through the resistor before going to the coil.

With points, the negative wire on the coil grounds and opens to build and collapse the charge. My guess is that an Ignitor I or II does the same. The positive is always hot (when the switch is in Run or Start).