The wires on the carb are part of the safety mechanism to prevent the machine from running if the carbs get stuck open when you let off the throttle. Disabling (disconnecting) them will not interfere with the engine's spark, but you will lose the extra element of safety if you ever get a pinched throttle cable or iced carb slides. It is possible that having those wires connected is interfering with the spark though if the switching mechanisms are not set correctly.