Airhound, The answer to your question " was it the wire/pin crimp connection, or the pin connector seating? Or…how do you think whatever it was with that pin it came about?"
A little surprisingly, once we found the pin and wire circuit with the continuity issue, the wire/pin crimp connection was fine. The problem was in the female side of the connector. We had to slightly squeeze the female connector so it was a slightly tighter fit with the male prong. Why this happened after 7+ years I am not able to answer. As you would expect, the secondary pump is powered by it's own separate circuit breaker and wiring.