I had similar issue on BLK line (high voltage drop), finally I found issue on corroded junction inside wiring loom : http://forums.sohc4.net/index.php/topic,176018.msg2048272.html#msg2048272
Just 2 weeks ago, when I was doing bike yearly inspection, I found that sleeve again full of water (probably from last autumn washing)!...so no surprise there were corroded junctions after 40 years
Back to you - do what bryanj suggested:
1. clean IGN switch
2. test with jumper lead to regulator blk terminal and if better then run new external blk wire to regulator
Thanks for the suggestion, Erny!
I stripped back the wire harness cover to where it branches by the coils. The junction of all the black wires looks great. It measured 0 ohms resistance and the voltage was the same before, at, and after the junction.
The original tape was starting to fall apart and I wanted to rewrap it anyway.
First thing i notice is you are loosing approx 1/2 volt across ignition switch which is not good. They can be taken apart and cleaned/re greased.
Second thing is battery voltage is dropping quite a bit with load on it which makes me think battery is getting tired.
Third is that the difference between ignition switch black and reg black makes me suspect a poor contact sowhere inside the loom.
Pesonally to test i would put everything together leaving the black off the reg and then when engine running use a jumper lead from battery positive to the connector on reg box that the black goes to and see what your charging does, not forgeting it wont charge till higher revs.
If that gives you a better charge rate i would splice a new external black lead between the black at ignition switch block on loom and regulator whilst looking for a better loom.
Bryan, I should have noted that when I measured 12.7v on the red wire at the ignition, the ignition was off, and when I measured 12.3v on the black wire at the ignition, the ignition was on.
I let the bike sit on a trickle charger last night since I was messing with it so much yesterday, but I went and retested the red and black wire at the ignition, and they measured the same tonight at 12.5v with the ignition switched on.
In post #16 I mentioned that I already dissembled and cleaned the ignition switch. Here are the before and after photos. I did not disassemble the switch any further than this, so if there's more to clean, please let me know. I also disassembled and clean the killswitch itself. It wasn't as bad as the ignition switch, but it was dirty. If I recall correctly, cleaning both of these gained just under half a volt. I think...

Also, here's the melted main fuse. You can see it's drooping a bit compared to the other fuses.

Tonight, with the bike switched to on for at least 30 seconds, killswitch set to off, and all the lights but the tach gauge light bulb unplugged, the measurements are:
12.6v Battery terminals
12.6v Start at battery lead on solenoid
12.57v Input of fuse
12.53v Output of fuse
12.48v Ignition switch red
12.48v Ignition switch black
12.44v Black and white terminals of the regulator
I really seem to get the biggest drop when the killswitch is switched to run and/or when the lights are plugged in.
It's flippin' cold in the garage tonight, so later this week I want to experiment with switching the lighting to LED since I have some LED lights I can easily steal from another bike and do some quick testing. I'll switch all the lights over and compare what I get for measurements and report back.
Is it possible to run the Dyna S electronic ignition with a set of OEM coils without issue? I still have my original coils. A while back, when I was chasing other problems, I thought they might be going bad but perhaps they're fine to use and maybe that will gain me some voltage. Hate to have money invested in parts that aren't being used though...
Anything else I can try while I wait for the stator to arrive?
P.s. - Thank you for all the help. I really appreciate you taking the time to help me get this sorted.