65 Barracuda electronic ignition, orange box, ballast resistor questions

The two blue wires are probably spliced together under the harness tape.
The diagram will show these as Ignition 1; which is the circuit for ignition and alternator power.
The brown wire is almost certainly Ignition 2, power for the coil and ECU when key is in start.
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From your pictures, my guess is the harness looks something like this.
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On your '65, make sure the battery feed/charge connects to the terminal leading to the ammeter. The alternator lead connects the terminal that leads direct to the main splice (big dot in diagram)

On the factory diagrams, wires starting with
J usually is for ignition circuits, but in the early 70s also includes switch feed.
R relates to alternator
A usually relates to battery