Thanks Tim.
A year or two ago the fan failed on a hot, slow ride home from work. I had steam coming out through the fairing and had to stop every few minutes to let her cool down, until the last six miles where I knew I could keep her at a constant 50mph (or 60 or 70 or...). I think I also had to replace the water pump.
I wired up a switch so that I could turn the fan on manually, but didn't remove the original temperature sensor wiring. Strangely, the next day the fan worked fine all by itself and to this day I've never had to use my manual switch. The fan seems to work fine all the time. I think the fan (including my manual switch) is activated by the negative not positive current.
Could I have affected something by putting in an extra earth wire?

I do have a suspicion that this will eventually be traced to some of the wiring mods you've made.

How do you know its working when it needs to? If there's a short in the motor wiring, how would you know it?

Yes, the motor is hot all the time when the ING is on, the thermostatic switch sends ground when needed.

What I'm thinking is that there is a short in the fan motor sending current to ground when the thermostatic switch closes the circuit. The motor would then act like a heating element draining the battery, but only during the periodic short.

As far as blowing bulbs goes, what I'm thinking is that when the fan shorts, and the ING is on and the fan is trying to pull current from the other fused circuits, the bulbs themselves, act like fuses (or weak points) and blow. That's why you are chasing ghost with blown bulbs.

This is just my opinion. I would start there.

I can hear the fan come on and see the voltage drop when the engine gets hot (temp gauge 2/3 to the right), and vice versa when it cools down a bit. This happens all the time in traffic. it doesn't come on at all when the temp gauge is below the 2/3 mark.

Might I add my two cents. If I've got the picture right the charging system works correctly - charging at 3500 rpm or so, the battery holds charge over an 8 - 10 hour period, but goes dead rapidly when negotiating heavy stop and go, slow traffic. There have been problems with the fan in the past, and suspicion falls on the fan.

If the fan bushings / bearings are worn there could be drag on the armature, causing the motor to slow. That causes excess current draw. So heavy traffic, low engine rpm/low output from the alternator and heavy draw from the fan = dead battery.

It would be interesting to take a ammeter reading at varying rpm with the engine hot and the fan running. Given that there is a manual switch it could be done with the engine cold, but it would be better to do it with the thermostaic switch in operation. Well, hmmm. Do the check both ways. Cold using the manual switch, and then hot with the manual switch off. Maybe the problem lies with the thermostatic switch.

My only question revolves around the statement that after a quick charge voltage was normal for the remainder of the ride. Was the remainder of the ride in lighter traffic, higher rpm riding? That could explain the normal output.

If not, well then all that is left is to deal with one of the harder to trace electrical problems - an intermittent open/short. Then you are back to checking all connections and grounds including fuses, inspecting the wiring harness for bare spots and checking the regulator/rectifier.

Sorry to blow a hole in your theory TBT but the fan circuit is completely isolated from any other electrical circuit on the bike. The only thing it shares on common is earth so there's absolutely no chance that the fan or thermostat are causing bulbs to blow. Yes, any part of the fan circuit could be causing an intermittent current drain in the form of a short to earth or excessive current drain if the fan motor is having a hard time spinning properly but hmmm seems to be suggesting that it does do what it's supposed to at the right time now.
One thing I can't understand here is how you wired in the manual fan switch. It seems strange that you say the fan works properly without touching the switch. Does that mean you'e wired it in line with the thermostat or did you run a new wire from the fan motor via the switch to earth? If that's what you've done and the new switch circuit is never closed but the fan comes on automatically then that proves that the fan circuit is working correctly. Flicking your switch to the on/closed position means that the fan would run all the time?
Remember, short circuits usually blow fuses. You're looking for a slow drain. This is starting to point more towards reg/rec failure or a bad connection in the charging side or a crap battery.

Thanks Henry.
ISTR I just ran a second wire FROM where the fan wire connects to the thermo sensor thingy on the radiator TO a new rocker switch I installed (in the fusebox cover). And yes, if I flip that rocker switch, the fan comes on.
I think the RR is OK; my battery is a new Lithium Iron one (which at the moment shows no faults on the dedicated charger); so it looks like it's a dodgy connection somewhere in the myriad spaghetti connections I now have.

OK Howard, fully understood.
Looks like you're in for the long haul, cleaning every plug connection and inspecting the whole lot from top to bottom. Bad luck. The good news is that if you're in the right head space and luck is with you you will find the fault. It's impossible not to. Back to the old how long is a piece of string again....
Keep posting. Your woes will always be a source of solace for others.