My bet is pick up gap is too small. With VA hooked up, the p/up coil is making contact with the reluctor. No spark is the result with mixture not combusting in that cyl. When the exh valve opens, the mixture is ignited by the exiting burning mixture from another cyl.....pop in the exh pipe.
Check the air gap, should be 0.006-0.008". Also check that the VA plate & shaft feels tight. Any movement might close up the gap.
