Troubleshooting fuseable link failure

It's got to be somewhere. Nothing you checked stands out to me.
To make it easier to follow, attached is a diagram for your 68 with the fuselink gone and the battery and alt disconnected.

.3 ohms from alt ground to engine ground may be normal. Compare the case to the ground your referencing. It will probably also be .3 ohms - in which case the resistance is from the case through the block back to wherever your probe is. (Battery negative cable is a good reference.)

The drop through the field - I don't know. The shop manuals test specs are in terms of power draw. The resistance you are measuring is from the terminal through the brush an contact ring, then through the windings of the rotor and out the other brush to the other field terminal.

You could rotate the alternator to while checking again. It's the output side that I'd be most suspicious of, but so far, nothing is pointing toward the alternator.

No other clues on the wires or connectors? Anything that shows signs of excessive high current (heat) ?
If the ammeter was working and you saw nothing abnormal, then it would seem like the short must have been before the ammeter. Might just want to take a look at the wire from J to the ammeter. Also that there are no other wires that could be touching the ammeter's battery terminal.

You can also check for resistance through the circuit. This would not show a short, but high resistance would suggest a long term problem. A circuit with high resistance draws more current than it was designed for. Over time the heat damage can cause additional breakdown.

It's worth checking the starter relay side of the circuit for a ground. Also the condition of the battery. I wouldn't think the alternator would supply enough current in a short ride to burn the link, but its possible. The ammeter should have been showing massive charging.

Worst case, if you can't track down a short, you can test hot using a circuit breaker. There's a Chrysler MTSC that shows how to do this.
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Regulator and Ignition circuits:
Was the check with the switch on? Although the only diff would be the wires to the main splice so I doubt it will make a difference.

Pertronix Ignitor: Where ever they suggest is probably fine. Coil side will have reduced voltage while running, full voltage when starting.

Electric choke: I'd think it would prefer full voltage. Also, I think it would be better to have this on a fused circuit.

Charging-diagram68BV-looking4short.png