Bulkhead wiring/fusible link questions

Not sure what you're trying to accomplish, But here's the fusible links are there to protect the charging circuit and everything withut a fuse from the battery shorting. Explained better here:
Fusible Links in Charging Systems with Ammeter

If you want to rewire the charge circuit without an ammeter, and distribute power from the battery, then you must fusible link each circuit coming off the battery. Thats when the 2 gages smaller rule of thumb comes in. Base it off of the smallest wire in the circuit being protected.

If you just want to get a better connection in the alternator and battery feeds, then take them through the firewall with a grommet with new wires. You can leave the old ones and run in parallel, or remove the old ones. If running in parallel, probably better to use one fusible link, but its up to you.

Bulkhead connector bypassed.
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Same but original wires retained (operating in parallel). See post 6 of original thread on Charger forum.
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P is the 12 gauge black wire alternator wire (and the most corroded looking connection)
Alternator output wire connects to the main distribution (welded splice) inside the car. If there is corrosion or other damage to the connections, this is where the voltage is being lost when the engine is running and equipment is on.

Q is the 14 gauge brown wire that connects to the ignition coil and the ballast resistor in the engine bay and (converts to 12 gauge) the start position on the ignition switch inside the car. What does this parallel connection do?
Not sure what you mean by parallel connection, perhaps you are you refering to the field power on the alternator?
Turning the switch to start sends full voltage to the coil positive.
Releasing the switch to run sends full voltage to the other side of the ballast resistor, so the coil gets less the full voltage and current. The run wire also connects to the field of the alternator and the voltage regulator. The regulator 'reads' the voltage available and regulates by allowing the field to complete the circuit to ground (green wire)

Basic circuit. ( Wire for powering coil when starting is not shown, but attaches to the coil side of the ballast resistor. '73 colors may be different.)
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I've been putting this bypass off for a while and hope to get it done in the near future. I have less than 11V in the car when anything is turned on (run position, headlights, whatever)
Running or on battery alone? Measured where? Look for the voltage drop from the battery (or alternator) if you want to find the locations of high resistance.