Your 2nd picture shows the unused dimple that was supposed to be for the C4 wiring. My '66 C4 firewall is shown in the attached picture.
A bundle coming up from the C4 NSS switch has 4 wires in it: 2 for the NSS and 2 for the backup light switch. Those break out into 2, 2-pin connectors: the light blue connector is for the red/blue wires on the NSS and the red connector is for the black/red wires to the backup lights. Those wires go through the firewall above and slightly to the left of the gauge feed connector. The dimple to the right is for the A/C compressor wire.
I don't know what that is in your first picture but it is not an original ignition resistor. All Mustang ballast resistors were a pink wire built into the wiring harness on the passenger compartment side of the firewall. The wire to the coil from that resistor was a red/green wire on the top row of pins in the engine gauge feed connector, 2nd from the right when viewed from the engine side. There is also a brown wire sprouting from the same position which goes to the solenoid to supply +12V to the coil during cranking.
I don't know what the wires running above the engine gauge feed connector in your 2nd picture might be. They aren't on either of my cars but I have a manual top.