So I removed the seat, tank and battery and cleaned all the suggested connectors and then some:
- fuses and fuse block
- ground at trans and under tank
- ignition switch wire connector
- ignition switch through key hole (set screw could not be removed to disassemble switch)
- battery terminals
- alternator connector
- starter lead
I did not see any frayed or burnt wires during all of this.
I allowed the bike to idle while I picked up the tools. The alternator light was perfectly dark for quite some time then just before the radiator fan kicked in the alternator light began to glow. The glow did not change at idle but got brighter as I fed in throttle especially above 3k rpms. As I let off the throttle and the revs dropped all the lights on the bike that I noticed (neutral and brake indicators in the dash, headlight, alternator light) flickered briefly and the alternator light returned to its dim glow.
Just before the fan kicked in the alternator light went completely dark. Just as the fan stopped the alternator light began to glow again. I'm thinking this may be a coincidence because when the fan kicked in the 2nd time the alternator light just continued to glow. The bike did not stall through all of this. Finally while the alternator light was glowing I shut off the ignition then restarted the bike. The alternator light remained off. This feels similar to my experience that when the bike does stall the ignition must be cycled before it will restart. I stopped the experiment at this point.
I should mention that when these issues first began I tested the Hall effect sensor by letting the bike idle and using a heat gun on it. I heated the sensor until it was too hot to touch without the bike exhibiting any bad behavior.
Also, last summer I had the alternator out to check the monkey nuts, which were fine, and disassembled and cleaned the starter, just before a 5k mile trip that went off without a hitch. Since then I've cycled the starter backwards a couple of times.
Any more suggestions I'm all ears. I have some time tomorrow to work on it and take it for a test ride but I think that's going to be about it for some time.
Thanks to all who have replied so far! Futility wins for today!