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Also seeing these wires on the left side between the tank and fork that seem like that might not be ideal

See the below pic for an explanation of the spare wires - now for the "important" bit. do you still have the bulbs out ? schoolboy error on my part (comes from dipping in and out when I'm supposed to be working 
You need to redo the voltage checks I advised on the orange wire at the flasher unit - I completely missed the fact that your voltmeter is on VAC and it should be on VDC which is why you where getting strange readings - apologies for 2second rate" guidance 

 

Glad to hear the loose wires aren't of concern and I put everything back as I was worried something would get lost or I'd forget what went where so it's all buttoned up but I want to say I tried it on that setting and got similar results. Just slightly different numbers. Is that worth tearing it all apart again?

How different where the readings ? If it's back together let's leave it that way for now. So reading back through the thread the fault has always occurred whilst riding - Try leaving it idling stationary on the stand with the turn signals on - you said it took about 10 mins last  time so try 10 mins on left and then if still ok try 10 mins on right - I still think the grey or green is shorting to ground partially (or something else is) try the static test and if it still blows I will give you next steps (which will involve taking it apart again)

stupid question but if it is the main fuse I assume you are using a 20amp fuse ? (generally they don't blow easy)

Yes it's the main 20a fuse each time and it's usually about 10-15 mins of riding but what amounts to 5-6 corners so I'll give it a shot standing in the garage but I've only two fuses left as they're apparently not very common and I had to buy a big multi pack just to get three in that size.

Ok, so I left it not running, but with the blinkers going. 2 full mins on the left, 2 full mins on the right. No issue. Switched on the high beams, one full minute each side, no issue.

Thinking back I did twist the adjustment on the flasher as it was very rapid and so now it blinks about what the average car would anyway. Any chance that was the issue, it blinking too fast?

ThatYeti wrote:

Ok, so I left it not running, but with the blinkers going. 2 full mins on the left, 2 full mins on the right. No issue. Switched on the high beams, one full minute each side, no issue.

Thinking back I did twist the adjustment on the flasher as it was very rapid and so now it blinks about what the average car would anyway. Any chance that was the issue, it blinking too fast?

Unlikely the speed would effect it, now try with it running and the flasher on turn the handlebars all the way left and right - what happens ?
are these the type of fuse you have

 

Not sure I'll have time tonight but will if I can, and yes except they're 25mm long which is apparently a very uncommon size.

ThatYeti wrote:

Not sure I'll have time tonight but will if I can, and yes except they're 25mm long which is apparently a very uncommon size.

That sucks, they are readily available in the UK (classic car scene) if it comes to it you can unsolder the ends and solder in some 20amp fuse wire

Ok, running for 10 mins now with blinkers going, turned left right no change. Only thing that really changed was the speed of the blinkers....is that possible?

ThatYeti wrote:

Ok, running for 10 mins now with blinkers going, turned left right no change. Only thing that really changed was the speed of the blinkers....is that possible?

Unlikely, I think what you have is a wire on the output side of the main fuse (everything except lights) that has rubbed through and either vibration or motion (bumps in the road etc) when on the move is causing it to short to ground (the entire electrical system doesn't draw 20 amps) so see how you go. If it is what I think it could take a bit of finding unless there is clearly visible damage to the loom somewhere. (it may have been the damaged headlight wires  )

As far as fuse availability, I updated the old glass fuse on my Z1 to more current blade type.  The old fuse holder plugs into the harness before and after the fuse.  You can find the blade type fuse holder pigtails at your local auto parts store (standard blade fuse or mini blade fuse type).  add the correct bullet plugs to the pigtail and it plugs right in to the harness.  I got the bullet connectors from cycleterminals.com