1. Not 100% sure what schematic I should use.
[any of the 68-70 diagrams, even later ones, will provide the schematics. Though switch locations may change, their schematic function doesn’t change].
2. The bike has been worked on before by a couple mechanics my dad knew over the years. For example, the positive ground that goes to the engine case is black rather than red as supposed to be. I have two solid white wires on one connector, a black wire, and a white/brown wire that once went to the three way key switch
[you have been riding the bike, so the black wire from the engine case presumably goes to battery
+ve? If so its just the colour of the wire is wrong/confusing you].
3. The gauge of wire could be higher
[well you could use solid copper bars instead of wires! There’s only a couple of places where higher gauge wires would possibly be sensible, neither should be concerning you at this stage].
4. Like the three way key switch I’m eliminating but now that I think about it, it could be better to leave on and have that one key switch turn on the headlights. I don’t know but some of the switches can be eliminated. It seems overkill.
[the 3-position ignition switch allowed for a parking light provision, with the pilot and tail lamps on, that’s why so many wires went to it. If you’re going to use a 2-postion ignition switch, it only needs an input from the battery
(usually bown/blue or brown/white) and an output to ignition and light switch].
5. There are many wires by the headlight or in the headlight which are just capped off like all the wires that went to the ammeter I disconnected. Some are just taped up and hanging. It’s slop.
[hopefully when you took the ammeter out, all the wires from both terminals were joined together?].