I replace the main wiring harness and all the sub-harnesses. I also replace all the electrical components. Since this bike sat for almost 25 years and the components and wiring were not in good shape, replacing it all should provide very good reliability. You can see how I remove what was left of the original electrical system here.
Here is a link to the documentation and YouTube video summary of how I do this work.
VIDEO: 1983 BMW R80ST Install Electrical System