Skull, that is really useful advice and an excellent reading list at post #12.
Dom, the thing to remember is that although the wiring and diagrams
look complex, they are in fact fairly simple once you see how each circuit works. Leo's guide to what happens when you turn the key is a good place to start thinking about the various functions - charging, ignition, lights, etc.
The wiring on my XS was badly mauled by POs and in the end I hauled it out and started again, from scratch, using a simple set up borrowed from the tech section. I think
@Adamc did something similar and has re-wired using Motogadget switches. Ripping out and starting again is the drastic way of getting a wiring system you understand. Also, usefully gets rid of a lot of components you don't need such as lights checker or turn signal cancel.
Short of that, I suggest taking notes and drawing diagrams. Get those coloured felt-tips out and draw a scheme for each circuit. For each wire that leaves a switch or component and disappears into the depths of the harness, learn where it reappears and you really will soon start to see what's going on. As has been mentioned, get continuity testing with a multimeter.
Good luck!