Good concept, Jim, but you won't be able to do a single installation guide "specific to the XS650." There were many minor changes over the years and a major change in 1980 when Yamaha replaced the early mechanical voltage regulator and separate rectifier with a solid state reg/rec module and changed the wiring to the alternator brushes.
Yes, I see that there have been several changes to a bike with as much longevity as the XS-650. I'm not sure that the charging system is really a big impediment to integration of the SSPB. Whether the XS650 has an mechanical or solid state regulator or has a field controlled alternator of a Permanent Magnet Alternator (PMA), the SSPB still connects directly to a single Red wire. This is in addition to the other direct battery connection through a fused primary lead.
In effect the SSPB separates the primary power flow from charging and battery from the harness. This is especially critical if you have a PMA with shunt regulation.
I think it is harder to grasp how to take a non fuse box harness and convert it to segregated Signal,Headlamp and Ignition circuits. If you have a fusebox then the following diagrams are really all that is needed for a basic configuration. I think I am going to revise some of the GS documentation to show the connection in a corresponding way.
For the non fuse box model, the whole schematic is required to show the breaks in those circuits; I have done that for most of the early years.
Here are the drawings for a basic setup on a fuse box model (stock and conversion to SSPB).
The primary benefits you see from here are that there is no longer any significant current running through either the IGN switch (only parking light power) or the Motor Stop switch. SIGNAL,HEADLAMP and IGNITION circuits remain segregated with equivalent "safe" solid state relays. So although there are some slight differences over the years as to how each of these circuits is wired in the harness, the connections shown at the fusebox will always be the same.
As is this is a minimum configuration, I have omitted the additional ACC channel for clarity.
In order to get the headlamp cutout from the solenoid signal, the wiring has to be reconfigured for high side control as is more traditional. If you don't have and Engine stop or a push button the SSPB defaults back to IGN switch control only. Of course because all power from battery and Alternator is routed through the SSPB it is fully protected "safe power" with the built in current and thermal limiting.