It's probably something "up stream" that is frying the box.
The number one suspect would be the Stator, although the trigger might also be the culprit.
Your "kill wire" (black/yellow) is simply the kill circuit (path) to ground so that when you want to stop/kill the motor (turn off the key, pull the man overboard switch, or flick the kill switch) the (power) stored in the switchbox will "go to ground" along that black/yellow wire instead of the "more difficult" option which would be to jump the gap on the sparkplug(s).
So if the motor is running their "should be" voltage in the black/yellow as part of it's normal operation - it just shouldn't be going to ground through that wire.