New owner of a 1981 XS650 and I don’t know where to start

I hope I am not confusing things here. It is common to have some voltage loss between the battery and the headlight shell/ keyswitch. It seems your charging system is doing well. Get a baseline battery reading at 3000rpm. Get a baseline headlight shell hotwire (brown on my 77 and 81 IIRC) reading. Figure your loss. My 77 and 81 are way different and I think there were maybe some wiring changes between those years. A $10 volt meter that I use velcro tape to mount tells me my charging system is or is not operating. I learned this on a Yamaha 650 Society rally in AK from @rhkansas in 2022. There is a ton of hard learned wisdom in this forum, I hope to absorb some of it.
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Your voltage readings (very thorough there!) are very consistent with my bike when I got a new rotor and put in the VR115 regulator.
my voltage goes as high as yours while revving though.
There is a screw that you can adjust the switch voltage for the stock regulator. That is documented in my 1978 special project thread with photos.
I however did not do the measurements w/ the Headlight unplugged like you did.
My light is off until bike is running (1978). I do have a switch that I can turn the headlight on w/o the bike running but I did not take that measurement.
I do agree you want to get measurements at cruising RPM. My regulator was set WAY too high before switching (16.5V). I claim that is due to the switch voltage being a mechanical spring that is adjusted and that the coil gets weaker over time and the switching voltage goes up. I also claim that is why my rotor and regulator burnt up. The battery likely failed on the Previous owner too.
Melnic ......

HL Switch Relay.jpg

This only works on the '78 models and is a very worthwhile "mod" in my opinion. You can easily change it back if you wanted to, but I don't see why you would.
Yes, there is a friction or "drag" clip on the #4 starter gear. This is supposed to slow it's rotation down so it will engage the gear on the crank correctly and fully. The clip spreads open over time and gets weak. Then it slips on the gear and doesn't slow it's rotation as it should. The gear doesn't engage properly then, sometimes only partially and sometimes not at all. The "fix" is to squeeze the clip tight again, details are here .....

This is something you may need to re-do every 5 or 6 years.
The starter works but slips. I know there is a tensioner spring or something that needs to be adjusted. I'll get around to it next time I change the oil.
I don't if it's clear enough, but the right side cover has to come off (kickstarter, brake lever and right footpeg have to come off) and the clutch needs to come off to get to the spring clip. I've done it a bunch of times, if you can get 5 lbs drag on the loop of the clip as measured by a luggage scale, you should be good. Squeeze the loop together, but put a 5mm or 1/8" drill bit in the loop so you don't collapse it.
Just a thought, but the starter may be filled with oil, and not able to spin fully... there is a seal and if it fails, oil gets into the starter. I had a very slow/hard starting "starter" motor and found that was the issue.... Replaced the seal and problem solved. May not be your issue, but I didn't see it mentioned yet. (Note: If I recall, it's kind of a pain to pull the starter)
(Note: If I recall, it's kind of a pain to pull the starter)
It's just one of the four bolts that helps you learn new words. Oh! Drain the oil before you pull it. With this bike, I think it may be just a weak spring. The ignition timing needs to be checked before tearing into it. As I recall, kicking it to life is hard work.