Pete,

With the symptoms you describe I'd be looking hard at the power supply board and the large filter cap before I went wild and replaced inter-board connectors.

Sounds like the load imposed by the snake pit magnet or flipper is causing the cpu reset.  The quick test is to measure the AC voltage across the filter cap to gauge how well it is performing. As performance of the filtering drops off the AC voltage will rise.  I'd also have a look at the reset signal test point on the cpu board - needs to be high, but you may not see it drop without an oscilloscope.  I'm sure this covered in the pinrepair guides.