Got it fixed and went for a ride, and it's working great now. Charges a little bit higher on the nighttime circuit than the daytime, and I could probably plug the tail light back into the battery, but I'll leave it on magneto for now. All I have to do is switch the wire at the tail light. After riding for about 5 miles the battery is at 6.3 and I started right around 6. At idle the nighttime circuit shows about 6.4 volts, and revved it goes up to about 6.9.

That broken wire is also probably why your headlight blew. 

Regulator is good insurance. 

Yep Mark I'm glad I have the regulator on there, I didn't know that they were supposed to have one added. I think you're right as well that that wire probably touched something it shouldn't have, and caused the bulbs to blow.

RT325 the pics I'm posting are not hosted, the site is working now.

Wire didn't need to touch anything.  Charge wire disconnected would have made more power available to headlight.  Same as running without a good battery installed (and no regulator). 

That makes complete sense. Without the battery absorbing that power, it's got to go somewhere. By the way, on the next page of my manual (from the one I posted earlier) it does mention an extra white/red wire that could be used to increase charging power, but my bike doesn't have that white/red wire. They also caution that if you leave it hooked up too long, you could damage the battery. I guess they only had that on the early CT-1s.

Yes, as I said earlier there is a Yamaha bulletin about the wiring error in the literature.

And I would say that what you just mentioned is the exact reason you should connect the taillight back the way it belongs...  These bikes rely on "balance" so when you start changing loads you are causing issues. Taillight bulb draws about an amp.  The battery has to absorb that extra amp without taillight draw and it does so by getting hot and losing water, especially on longer rides.  (Keep a close eye on battery water level as it's likely to get low fairly quickly if it is overcharging.)

Even the missing gauge illumination bulbs which are on the AC headlight circuit...  only a few watts...  get you that much closer to burning out a headlight on a bike without a regulator.  (Won't matter now that you have a regulator... unless Scotchlok fails)

I get what you're saying Mark, but what about the bikes in other markets like NZ that didn't have to abide by the 15 minute rule? They have the tail light on the mag. I kind of like the tail light on the mag because I get a much better contrast between it being a daytime running light, then a very bright brake light. That said, I'll experiment, and plug it back in, and see how it is with the bad charging connection repaired. Learning as I go...

Apples and oranges. 

Early CT's didn't have battery taillight either.  But they had different wiring and charging systems...  they were designed to be run that way.  Much simpler layout.

If you like mag taillight, you should probably use the daytime charging wire for both day and night.  Just don't use the green/red and jumper the day charge wire over to where green/red was. 

That's a great idea Mark,, but I think instead of jumpering the daytime circuit I'll just swap the wires. Then I'll have the daytime charging circuit when the lights are on, and if I need to do a fast charge I can turn the lights off for a while. Then if I decide to run the tail light on battery I'll just switch them back. Eventually I'll put a new sealed beam in and replace the instrument illumination lights.

The first CT1s might well have come with headlights with replaceable bulbs and I would venture that the part number was 251-84120-61 (see link below).

2518412061: Lens Assy Yamaha - buy the 251-84120-61 at CMSNL

I've probably got one of these (it came fitted in a very early CT1 headlight bucket) - the Koito part number is 110-31837 and a couple of photos are attached.

The light itself won't be fantastic, but the bulb will match the lens and the lens will fit into the existing ring.