Ray, we all hate electrical problems like that. It destroys confidence in the bike and it's a HUGE mystery. I'm afraid the only solution is a thorough going-over of the complete ignition system - unless the source is located earlier.
Troubleshooting is something of an art. It's almost a scientific thing and if you can get into the swing of it, almost fun. The first step is having something of an understanding of how the thing works. With that understanding, figure out what could possibly keep it from working or cause that particular fault. Then start looking, checking and measuring.
In some cases, experiments might be called for. Try to eliminate many items at the same time.
I recall in the manuals I had in the 60s and 70s lists of items to check in the case of certain faults. Some of the items wouldn't apply to the fault at hand and I'd have a 'feeling' for what it could possibly be and jump to number six right away, rather than checking the first five in sequence. Sometimes that worked - sometimes not. But the better you know the system - and that particular system specifically - the easier it is troubleshooting.
This is a chance to get acquinted with your machine intimately. You need more data to locate the fault, right? A rule of thumb that works very well with me is: when in doubt, more data is needed! Substitute mystery for doubt and it might make more sense. You just don't know what's going on, so you need more data. Well, the data is in books, wiring diagrams, on forums like this, and can be gotten with your eyes inspecting the bike. Perhaps some data will come from having someone else look at the bike - someone who knows these things well and knows what to look for.
When I've got a problem like this, I just start straightening everything up. I fix whatever I see, whatever doesn't look right to me, or non optimum. Maybe it's something totally disrelated, but after getting that fixed, get back to the electrical. Make sure wiring is secure so it can't flop around - zip tie it securely to something stable. Make sure wiring isn't chafing on anything and could rub through insulation. Make sure connections are clean and bright. Do the wires look neat and tidy? Clean it all up, and re-route wires so they're pleasing to look at.
As for experiments, maybe the kill switch could be eliminated from the circuit to see if the fault goes away. Figure out how to do that. Or perhaps you get the idea it could be the ignition switch - how could you prove that? Maybe hot wire the bike (eliminate the switch from the circuit entirely) and see if the fault goes away.
But the thing that makes it the most difficult is not understanding how everything works in the first place. I know, it's a real bitch - but you've got to start somewhere. And I know from my own experience, electrical was the last area I felt comfortable with. It was the most difficult to understand. But the more I dealt with electrical problems, the more I learned and eventually I could think with it. Looking at a mechanical contraption with levers and gears - I could figure that out. Just look and see what affected what and eventually I could tell what wasn't causing something to happen and figure out how to fix it. But you look at electrical stuff and you don't see anything moving. You can't see little electrons speeding along from the battery and say - oh, they can't make it past that little bit of corrosion - There's the problem! No, a Volt/Ohm meter is needed and a knowledge of how to use it. But a lot can be done just by tidying everything up and making everything YOU CAN SEE as neat and clean and easily confrontable as possible. In the process you'll accumulate data and figure it out. Usually you'll know when you've found the problem, and like those bike adventures where a lot of miserable stuff happens, you won't be forgetting the story any time soon.
I remember the time the trailer lights wouldn't work right - we had to go somewhere on a long trip, and spending four or five hours trying to figure it out...
