Here's a few notes on my bike to start with:
-1979 xs650
-stock stator/alternator/reg-rec
I went off of this guy, as it had the same reg/rec-stator/alternator wires as my current (what I believe is stock) setup
From your pics, looks like a later alternator was fitted to your `79, which originally used a grounded rotor powered by a mechanical regulator. You should now have a powered rotor grounded by a semiconductor regulator, as on `80 -`83.
So the section of your last diagram using the one-piece rec/reg is okay.
Although I don't see the grounding-bridge type inner brush holder, you would want to ensure that BOTH brushes are not connected to ground. This could happen if someone used or retained the older brush holder block, where the brush clip screws could screw into the grounded alternator housing.
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