The one wire from the A terminal of the regulator that goes to nothing is probably for the ignition noise suppression capacitor. Leaving that disconnected won't affect the charging system, but you'll want to make sure the connector doesn't short to ground against any sheetmetal. It's un-fused and hot at all times.

The other wire from the A terminal that goes up through the harness is probably where power is coming from. To make sure, disconnect the battery (negative cable first, positive second as always) and test for continuity between the inside of that little plug coming off the A terminal, and the positive battery cable. That will tell you if it ends up being connected, without having to peel back your harness.

Take a quick look at the first diagram in this post, it shows a generic diagram from a Ford shop manual: https://www.ford-trucks.com/forums/9...ml#post9243162

The aftermarket choke should connect to 12-volts hot-in-RUN, and it should be a fused source. My '79 has a 2-connector pigtail hanging from the firewall near the heater box; this used to connect to the stock carburetor. One signal connects to the stator terminal of the alternator, and went to the factory choke. The other is hot-in-RUN and powered the original idle stop solenoid. It's also protected in the fuse panel. I use the latter of the two and I recommend you do the same. I don't remember which color was which, but you can easily check with the engine OFF and the key in RUN and test which one has 12 volts on it.