Just keep in mind that the battery voltage and fuse block are not involved in generating ignition spark. You can disconnect the battery and wrap a rope around the flywheel and pull start the motor. It will run just fine. The ignition system is self contained. The only thing that the battery voltage is used for is the starter, any accessories and the Tilt/Trim pump.
If you have intermittent spark, and you've eliminated the Kill Switch by disconnecting it, then take a look at the wiring on the terminal strip where the ignition system components (CD Modules, trigger, stator etc) are connected. Take a close look at the spade lug connectors. A lot of these connectors have a short piece of black heat shrink over the crimp/soldered area where the wire is connected to the spade lug connector. It's not uncommon for the wire to break right at this joint. The black Heat Shrink covers that area, so you cannot see the break. The Heat shrink holds the wire to the spade lug connector so you get the impression that the connection is solid, when in fact it's intermittent or maybe hanging on with a single strand of wire.
The trigger wires a more prone to this problem as they are made up of very fine strands. If you have the black heat shrink on your connections, that's a good place to start.