Hi Justin,
Welcome to the forum. I also have issues with my 66 coupe wiring and have decided to rewire it myself by purchasing a wiring harness.
Mind you, I have not done a rewire before, so I'm talking theory here... there are much more experienced people on the forum than myself who may offer better advice.
The research I have done suggests that if you're mildly handy and careful, it's not that hard to do. A harness made for a 1966 starts at around US$650 and up. Alternatively, you can get universal harnesses (not made for a specific car) starting at around US$200.
The issue with a universal loom is that you need to cut it to length and solder connectors... not to mention that it would not match wiring colours, so it would not be appropriate for a concourse car.
Anyway, that's my AUD$0.02 worth. I'll be interested in following this thread to see how you go.
cheers -- randall