I'm going to take a new picture in a little while and show exactly what I'm asking. 

Probe 1 is in the connector that the ignition coil plugs into (unplug coil)

Probe 2 is touching the black/white wire at the ignition switch plug (unplug ignition switch)

These two places in the harness should be connected so you should get same reading on your ohmmeter as when you touch the probes to each other (which you said was 0.00.)

Good morning MarkT,
The number 1 in your Pic, the wire on my harness is solid black ,I touch the black probe to it, other probe to black or black/white in the key connector harness side 0.00

My key connector plugs have only 4 wires red ,brown ,black and b/w

I just tried the black probe ( like in Pic 1. and other probe in connector to b/w 0.00 in the off position on the kill switch and 1 in the run position . Could it be that the black wire on my harness that plugs into coil little wire is meant to be B/W?

John,  

I know it's confusing that Yamaha used black and black/white  in the ignition circuit.   The little wire that the ignition coil plugs into is definitely the black/white circuit though sometimes the actual wire is black.  

And again, it doesn't matter that yours doesn't have two black/whites in key plug.  That's just a construction difference.  Your black/white to the handlebar kill switch is simply connected to the black/white at the key switch inside the harness someplace instead of at the key switch plug.

I should have asked you to disconnect more harness plugs to do that test....  could you unplug the plug with the black/white that connects to the stator on the engine?  And also disconnect the second kill switch on the handlebar.  Key switch and ignition coil should also be unplugged from harness.

Now check for continuity again between the black/white at the key plug and the little black wire you unplugged the ignition coil from.  Should still be 0.00.  

With the stator plug(s) disconnected the points and stator coils will be disconnected, now test the solid black at the key switch connector to the little wire at the ignition coil.  You should no longer get 0.00.  You should see 1 now.

Then check for continuity between the black/white wire the handlebar kill switch plugged into and the little wire to the ignition coil.  Should also be 0.00.  

You can also check between the black/white in key switch plug and black/white that connects to handlebar kill switch.  Again, should be 0.00.

Last test...  check the solid black wire in the key switch plug with one probe and connect the other probe to a good ground, say the engine case.  Do you get 0.00?



 

Ok, i unplugged the connector plug that goes to the stator over near my oil tank. Disconnected kill switch ,disconnected key switch and coil small wire, i get a reading of 1.
When testing the black wire in the key plug I get a reading of 1.
Black/white that kill plugged into in headlight bucket to little wire attached to coil I get 1.
B/w in key switch plus to b/w that connects to kill switch I get 1.
Solid black in key switch plug to crankcase I get 1., in the on or off positions

My answers are in the order you asked for

So one probe touching key plug black/white and other probe touching the wire connector the little wire to the ignition coil plugs into you had 0.00 before but now you have 1? 

Do you still get 0.00 when touching probes together?

Two statements are also not clear.

"When testing the black wire in the key plug I get a reading of 1."

Black wire in key plug and where else?

"Solid black in key switch plug to crankcase I get 1., in the on or off positions"

All these tests are on the main wiring harness.  If all the switches are actually disconnected from the harness, why are you turning switches on and off?

Mako is still working on the picture issue...  I think the best thing to do next is to post how to use a third party picture hosting so you can show us some pictures of what you're doing.  Someone did that a while back already...  I'll probably just try to post some screen shots of how I do it.  Busy at work so it will be a while


 

Ok I unplugged  the stator near the oil tank 
unplugged the kill switch at the handlebar 
unplugged the key connector 
unplugged wire to small coil wire
I still get 0.00 when I touch probes together.
 Ok, 1 probe on  b/w at key connector other probe at black that plugs into small wire at coil ,reading is 1 . It was 0.00 before i unplugged everything,  and i just plugged kill switch and stator plug back in, took a reading b/w at key connector other probe to wire that plugs into little wire at coil and got 0.00 in off position and 1 in on position on the right handlebar kill switch  (just to check myself) .
Ok, 1 probe to the solid black in key connector other probe to engine case I get 0.00
Ok, 1 probe to the b/w at the handlebar kill switch and other probe to wire that plugs into little wire attached to coil in the run position I get 1., In the off position I get 0.00.
Ok, probe B/w in key switch plug , probe b/w at kill switch reading is 1. In both run and off positions.
Ok, Probe to black wire in key connector other probe to crankcase I get 0.00 . I doubled checked all those test , i am sorry for confusing this 
thank you for everything 
john