If you "ohm it out" you'll find that the harness male red goes to one of the female reds. (it's just a short jumper wire wrapped inside the harness tape) The other female red goes to the key switch.  

Hooking the factory fuse to the two females gives you a fused connection between battery and key...  hooking the battery to the female that goes to the key switch is dangerous in that you no longer have a fuse and you have a male wire on the battery + which when disconnected could easily short to ground.

I'm not sure this detail would be in a wiring schematic...  I don't have time to look now but I think the error is something else.

Here is the Wiring Diagram correction:
 





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Thanks Mark, very helpful and solves the myterious orange wire I've been puzzling over. I brightened it up a bit in case there are others here like me that have trouble reading low contrast charts and diagrams. 

Thank you so much for the new info!

Thank you so much for posting this!

Hi Folks,
So still some puzzling questions! PLease don't shoot me if this seems simplistic, but still struggling with the wiring diagram.
Question #1: I have connected the battery as per everyone's recommendation. HOWEVER, I sould be getting 6v at the rectifier without any switches being turned on, and I am not. And yes, the fuse is good. Am I correct in my assumption?
Question #2: the lighting coil converts AC to DC so the blinkers, horn and tail lights can be fuctional (the headlight being AC does not utilize the coil I think). If you turn the main switch to the "on" position, will the blinkers and horn work without the motor running? I am thinking "no" iif the lighting coil supplies power to these lights, but "yes" if the coil does not.
I am really trying to solve this on my own, but for all I know the previous owner may have screwed this all up and was looking for someone to correct it.
Thanks again for your patience!

Indicators, horn, brake light and, I think, tail light should work without the engine running - ie off the battery. 

Red wire is a straight shot from Battery + to rectifier.  You should have 6v on the red wire at the rectifier and Zero Volts at the white wire on the rectifier without any switches on.

Lighting/charging coils put out AC voltage.  Rectifier is what turns AC from charging coils to DC by only allowing the positive voltage of AC on white wire through to the red wire to charge battery.  Rectifier also prevents battery voltage on red wire from backfeeding into stator white wire.

If you think of voltage as pressure and electricity in wires as water in pipes...  the rectifier is like a one-way valve. 

If pressure is zero on the "in" side (white wire, engine stopped) then the rectifier stops the pressure from the battery (6v) from leaking into the white wire.  When engine starts, the rectifier only allows the positive pressure pulses from white to get to the red wire.  Very basic way of DC charging from AC source.

With key on, all DC items will operate if you have a good battery connected properly.  This is everything except the headlight and gauge illumination lights..  the headlight and gauge illumination lights operate on AC right off the lighting coil with engine running.

Thank you! The wiring on this bike must be pretty fouled up. although it looks proper and in order. I must now rethink how I have connected the battery. There is only 1 red wire in the battery area that goes directly to the rectifier and that wire must go to the battery. 
One of the members stated that this wire is fused as a result of the other 2 red wires in the bundle connected together via the fuse. I am not sure how this can be, but for certain I have it hooked up incorrectly now.

It's only confusing because you can't see inside the harness wrap.

As I said earlier in the thread, there is a male red coming out of harness that is a short jumper wire to a female red.  If you unwrapped the harness tape it would fall on the floor.  Use your ohmmeter to find it. 

The other female red goes to rectifier and key switch. 

Battery female < < Harness male red short jumper inside harness ending in female red out of harness < < Fuse holder male to external jumper with fuse ending in second Fuse holder male > > to second Harness female to rectifier/key.

It doesn't matter how you connect the fuse holder between the two females...  can't screw it up.  then male from harness is left to go to battery.

If someone has hacked the harness, then you can find the internal harness jumper wire with your meter, connect one side to battery and other to fuse...  then other red out of harness goes to other side of fuse.