the ignition circuit should be rated to carry 5a continously.. even though in practice it will see less.
Was your toggle switch and wireing rated very low?
If that has a 6v sidemount coil, with no external resistors, and it was run on 12v, then there was more than designed current flowing.
points may have been welded or coil primary shorted.. or some other tomfoolery with the wireing up there causing a short.
i'd pull the genny and see if it passes a motor test. if it does.. I'd be inclined to put her back as 6v positive ground, with a genny.
In the meantime.. check your points and rig up some temporary better wireing and see if you can get her started to judge condition before sinking money into her.
got any spare coils or coils and resistors laying around?