So there we are.  Bare bones of electrical system connected up and battery connected.  No switches other than ignition switch connected and I am going through my voltage checks before continuing further.

Readings taken at main harness side of ignition switch plug unless stated as taken at the flasher can three pin plug.

Battery live to red wire at 6.4v. 
​​​​​​Switched live (brown) 6.4v with ignition switch on.
Switched live with switch off.  6.4v.  What the feck?
Unplug ignition switch.
Brown wire still 6.4v.  Not the switch.
Unplug red lead from rectifier.  Brown still at 6.4v.
Unplug flasher can.  Brown at a few millivolts.
Check brown, brown and white and ground at flasher can plug.  Millivolts.
Plug ignition switch back in. Flasher can disconnected.  Ignition on, brown at 6.4v.
Ignition off.  Brown at millivolts.  Switch is working fine.
plug rectifier back in.  Brown at millivolts.
Plug flasher can back in.  Brown once again at 6.4v.  Unplug ignition switch again.  Same result.
Pull flasher can plug again and check voltage at the three terminals again.  Millivolts.

I must be missing something.  It is obviously flasher can related, but I don't see how the flasher can is putting 6v into the switched live circuit when the switched live is not active to put power to the can in the first place and not one of the three plug connectors are showing 6v when disconnected.

Battery negative is connected to a good ground as per spec and the main harness ground ring terminal is also connected to a good ground on one of the ignition coil mounting screws.

All the wires in the main harness were checked for connectivity before fitting it.

Anyone else encountered this?  It is very vexing.

Found the problem.  Looking through the manual, the little info it gave was it was a "condenser type relay".

Hmm. Condenser = Capacitor.

I discharged all pins to ground  in case the capacitors were holding a charge, reconnected the plug and tested the switched live circuit.  Showing Millivolts only.  Just background stuff.
Switched on the ignition switch and tested brown again. 6.4v.

Switched off the ignition and brown was holding 6.4v.

Disconnected battery and brown was still holding 6.4v.

It is the capacitors holding their charge.  With nothing connected to the switched live circuit, there is nothing to discharge them.

Had me scratching my head for hours.  If I connected everything up first, it would not have happened.

Have I ever mentioned my luck?

At least everyone knows about it now.
 

Wow. That's a new one. Thanks for posting!

I wonder if it would have happened with an old-fashioned analog (swinging needle) meter? I have a couple digital meters that give me screwy (sometimes "impossible") readings at times. First thing I generally do is get out my trusty old Simpson analog meter.

(To be fair, my digital meters are not made by Fluke or any other high-end brand... analog and digital meters definitely have different characteristics though... analog is far better at detecting changes instantly (like points opening) than most digital meters.)

Yeah. I have dug out my old Yamaha pocket tester from the bottom of my toolbox drawers, blew the dust off it and brought it home ready for when I finally get around to setting the timing.  Not been used in 20 years but it is still working and the battery was still good.  I did change it though.

My all singing, all dancing, autoranging multimeters are hopeless for stuff like point setting.  They take too long to settle and are too sensitive.
A refugee from a time when times were simpler. She has seen a fair few sets of points in her life.

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Are you saying the flasher relay is holding voltage--albeit not for long i guess--. I remember MarkT saying be careful with those original 3 pin yamaha relays as can give you a belt if not careful. Are they just capacitor powered-activated. I don't know what i'm talking about--but googled & this popped up first thing. Or am i confused.
www.kawasakimotorcycle.org/threads/signa...uf-capacitor.192402/

Yes. The flasher relay was powering up the brown circuit, certainly for an hour or more when I checked because nothing was fitted to discharge it.

I jerry rigged the neutral lamp bulb up so it would light when I turned the ignition switch on and the problem went away.
The bulb discharged the capacitor immediately battery power was switched off.

I have one of those genuine yamaha multi tester ohm meters which i've had since forever--early years--but accidentaly tested my hot water cylinder resistance reading 'ohms' without turning off the 240AC volts power feed by mistake. Not sure what the hell i was thinking, just thought i'd turned it off i guess. Anyway--POOF. Might be an easy fix, i'll drag it out again. Loved that meter.

That would likely explain a similar issue that I had on one of my RDs.

Whilst trying to track down what was heating up the black wires in the harness, I chanced upon, whilst circuit testing, power in the brown switched brown wires, even when the ignition switch was off - ie my tester lit up when I connected brown to black. I did consider that a little odd! 

Anyway, I tracked down my issue to the red/yellow wire (for lights) in the left switchgear shorting against the switchgear body - once this was sorted, my warming up black wires issue went away and I thought no more about the brown and black wires circuit until reading your thread. 

Thanks for posting the problem and solution.

I wonder if the relay only gets a potentially dangerous level of undischarged power when the indicator switch is used?

The capacitor is charged when battery power is applied to the brown circuit.  When the main harness is connected to all its devices, it will discharge itself immediately through the various switches ect when battery power is switched off. 
Notably the neutral bulb or if a brake light switch was operated or in the case of later US bikes, through the always on lights.

On a positive note.  At least I know my main harness is not leaking to ground internally!