Thx Warthog, yeah there was plenty of smoke and melted insulation but the fusible links held.
Looks like maybe the long cranking 'did in' a battery. The alt1 was tested and fried, but the new alt1 also got hot, so maybe a battery. Switched the two batts around and now alt2 got hot. The battery charger didn't show any major amps going into the 'suspect' battery.
Where is the Voltage Gauge diode physically located under the dash? Voltage Gauge is out since this all happened.
Doghead relay mod was done immediately after the smoke cleared, too late for the alts and battery.
Surprised that a fusible link or two didn't get fried.
It is possible to have a voltage spike hit GEN1 and toast the rectifier or voltage regulator.
How long was the GEN1 running when it got hot? I'm assuming the engine was still running when you where pulling the cables.
If the engine is running, the alternators are producing electricity and when the cables are removed, there can be a voltage spike.
Have you ever rebuilt your alternators? It may be a good idea to plan for a rebuild in the future.
You need to breakout the voltmeter and check the output of both alternators and battries. Just becuase the light went out doesn't mean the alternator is working.