Hey Bo, this may sound elementary, but have you tried raising the hood in the dark to check for leakage, or tracking from the wires or boots? It takes 20kvolts to jump an arc 1", @40kv that's a 2" arc. I have found bad boots and jackets shorting to the nearest grounds, (i.e. valve cover, screw, etc.) by just opening the hood in the dark. Have the wife rev the engine if need be.
I had one arc to the valve cover where the insulation started to break down on the jacket. Couldn't see it in the day light but it glowed in the dark.