Some of your issues, perhaps #1 and #2, might be due to a faulty '12 Logic card; try swapping that out as well. As for the overload LED, it's driven by the VCA card, so it's not surprising that it doesn't come on when you pull that card. Try probing VCA card pins 34, 36, and 38 to see if in fact there's an oscillation that's triggering the LED.
Chris