http://www.cj-2a.com/oldsite/elec/wiring/index.htmlCheck this again, your alternator conversion sounds like it is the one to the far right of the next to last drawing.
Then look at the drawing immediately above the charging system drawing, and note that Sean states that even with the key off, the starter, lights, and horn still operate.
What that means for you is with a two terminal ignition switch, one terminal is always hot with voltage. That is the terminal your starter , horn, ammeter, and lights all hook to. �The other terminal, the switched one, is the one your ignition circuit is built to connect to, so that when you turn the key on, you have ignition, and when you turn it off, it is no longer fireing and the engine dies. � You will still need some sort of starter switch to activate your starter solenoid when you use the two terminal ignition.
What does your ignition switch look like again? And what are you using the fusible links for? If you are using them as fuses to protect wiring, just use fuse holders and fuses. If you are using a fusible link as an ignition resistor, it would go in the wiring between the ignition switch and the coil, and it must be natched to the coil .....