For what it's worth, I just finished rewiring my bike from scratch. All my electronics (battery, starter solenoid, ignition, regulator, rectifier, etc) now live in a shallow tray beneath my seat. All the wiring (including two new relays for the headlight) is located on the frame, wrapped in weather-proof sheathing. The only thing in my headlight bucket is the headlight plug, and it can be quick-disconnected.
It can be done. It just depends on your motivation and patience