Fuses are rated to protect against current, not voltage. I'm not really sure how much current the coil draws under normal conditions, so I can't suggest a fuse rating to protect it.
Both of those bikes should be 12V systems. The 6V is easy to identify, as there will be a finned aluminum heatsink mounted below the headlight, with a zener diode. No zener, no 6V system.
I don't have a 12V magneto here, so I can't tell you exactly what happened when you made the connections you describe. The 12V wiring diagram is as bad as the 6V diagram - much missing information about how things actually work. It should be a good guide on how to connect the wires, though.