Congratulations!  Things like that can be hard to find.  Great job!

P.S.  Nice video.  And VERY clean bike!  A+ work.

Mark - thanks for the advice, it really did save me hours and I probably would have jumped the blue/white wire rather not knowing charge coming from lighting coil. Question: What would be the result of wiring AC spark coil into the brown DC wire? I think I did that messing around with original wiring trying to rig it up before I bought a new/old wiring harness. I connected into brown It ran like crap for about 5 -10 seconds before I stopped it and rerouted coil wires (ground went into brown)- since then its way harder to start almost like timing has jumped (also get a backfill while starting). Will be running that problem down next.

That really isn't the correct ignition coil is about all I can say.  It's actually surprising it works as well as it does.  It might fail on you.  I've had good luck with original stock Yamaha magneto ignition coils...  but since you don't have one the best aftermarket I've found is this one that people here recommended years ago.  www.amazon.com/gp/product/B00230959C  There are a lot of new coils sold out there on ebay and places that are complete junk.

I can't think of anything that would make it act up like you described that would have happened due to your "experiments"...  polarity could be reversed (spark might jump from ground electrode to center electrode instead of center to ground like it should)  Also check your plug gap.  Should be 0.020" to 0.024", out of the box new they are generally gapped much wider. 

I too think you a 6volt coil

Broken black ground in the harness.--Thought you had a new harness, but i'm likely lost trying to keep up haha.
To kill the ignition i'd say the black white at the switch should join to black at the switch in the off position, bit of a guess but i know that would short it to stop.
So if switch black 'is' going to earth via loom then if you hooked black-white into the double female you have on the mag black at the coil orange--'or brown' then gotta stop it.
Be interesting to compare the primary resistance of the dc coil compared to the single wire ac coil.
I guess the dc one is higher which might show what a good mag you have powering into it to have it working good.
Don't get sidetracked reading my theories when Mark has it by the tail.
If ya coil gives out i have a few spares lol.
photos.app.goo.gl/ZRitJYJLgpgcCfup9
I'm a page behind, too slow to catch a cold.

Yamaha V50 scooters down here in the early "70's inNZ had a 6 volt AC single wire coil that looked identical to your 12 volt two wire DC coil if you could find one--fitted up inside the pressed steel scooter frame--same mounting to make it easy, but i've given up looking as had no luck at all. Much later V50's were CDI so likely change the coil & way its mounted. Any single wire magneto coil will do pretty much, or a single wire coil from a CDI mag system but will need to adapt it onto where it mounts. Maybe i've just been lucky swapping things around in the name of saving money.

More than you ever wanted to know... 

While the "lighting" might be 6 volt, the ignition coil on a magneto Yamaha Enduro is technically not.  It operates on hundreds of input volts.

Early Yamaha's had a standard magneto. Similar to the arrangement on a Briggs and Stratton Lawnmower engine where the ignition coil was driven directly off the magnets on the flywheel, on the Yamaha there was a small ignition coil under the flywheel with the large HT lead going from that coil under the flywheel right to the spark plug.  (My early YG1 and MG1-T have this type of magneto ignition)

Very soon after that, Yamaha upgraded to the "Energy Transfer" or "ET" magneto.  This is the type we are all familiar with on the Enduros.  It has a source coil under the stator and a separate ignition coil somewhere else...  under the gas tank on the Enduros. 

An ignition coil is basically an electrical AC transformer.  Transformers work on the principle of "induction".  There are two fine-wire windings in an ignition coil... the primary winding and the secondary winding (we've all probably tested those with a meter). 

On the original AT1 with the 12v generator-starter, Yamaha used a battery powered ignition exactly like most cars used to have.  It's invention was credited to Charles Kettering, founder of Delco and also of GM fame... often called a Kettering ignition.  How spark is created with the Kettering system is the primary winding of the ignition coil is "charged up" with battery voltage with points closed.  This creates an electromagnet out of the primary ignition coil winding with a magnetic field that encompasses the secondary windings of the ignition coil.  When the points open, this primary winding magnetic field quickly collapses which "induces" voltage in the secondary coil winding.  Since the secondary winding has many more turns of wire, the 12v primary voltage is "stepped up" to tens of thousands of volts when the magnetic field collapses.  Viola!  Spark.  

(Sidebar: when points close, the battery starts charging up the primary windings again.  Because of the relatively low battery voltage, the build up of the magnetic field happens too slowly to induce a spike of high voltage in the secondary windings.  Some may remember "dwell meters".  They measured how long the points were closed.  If you had too little dwell, the primary windings wouldn't have enough time to charge completely and the result was weak spark.  Not important on a Yamaha single as there's lots of dwell with points opening once per crank revolution...  but could be critical on a V8 where points are opening 4 times per crank revolution.  Too much dwell can overheat the ignition coil which is likely why the AT1 has a relatively wide points cam "bump" to keep the points open longer)

On the Yamaha ET magneto, the process is similar but opposite.  A transformer (aka ignition coil) doesn't care if the magnetic field is instantly collapsing (as described above when battery ignition points open) or if a surge of voltage instantly creates a magnetic field in the primary windings. Any instant change, collapsing or creating, of the primary magnetic field will induce voltage in the secondary ignition coil windings. 

On the "simple" ET magneto, the coils and magnets are carefully timed by design.  Spinning magnets around a coil induces AC voltage in that coil.  The Yamaha magneto ignition source coil and magnets are timed so that when the points just open, the AC voltage in the source coil is right at maximum. This instant spike of about 90 to 300 volts or so hitting the primary winding of the ignition coil creates a sudden magnetic field around the primary winding of the ignition coil which induces high voltage in the secondary winding.  Once again, we have spark. 

The ET magneto is very similar to a CDI in operation... points opening "discharges" the relatively high voltage from source coil to the ignition coil.  Capacitor Discharge Ignition (CDI) "discharges" the high voltage stored in a capacitor to the ignition coil when an electronic switch is triggered...  which is why an ET magneto is sometimes called a "mechanical CDI". 

Thanks to all for your prompt, useful, and informative advice.  You guys rock! As a result I just tested the bike and it seems to be performing like it's supposed to.  I did not install the battery, turned one click and engine fired -  no lights, turned to second click and lights are on, no horn (which tested OK earlier with battery jumped wires to it).  And the bike even turns off when the key is off!!!  This "new (off 69 model bike)" wiring harness even has a  blue wire that I was able to place into the speedo and there is a light!  The original condition had no lights going to speedo or tach, including neutral (which I need acquire).

QUESTION:  Since everything seems to be working (I am going to change out the coil as advised) fine, can I bypass using a battery and power the horn from the green wire at lighting coil, or red wire from rectifier? (I haven't checked to verify the rectifier is working or what it's producing - it was included in the wiring harness).   I would love to abandon the battery if at all possible as  the AT-1 12V battery box is cavernous for the little 6V battery I purchased to replace it.

Thank you!
Marshall

 

Problem is the original system used the battery as a rudimentary voltage regulator...  more of a voltage sink...  without one you'll likely blow bulbs including the headlight.

They didn't have voltage regulators so the system input is balanced against the load to keep the voltage in check.  No battery upsets that balance. 

Mark - Thanks.  I'm going to Ebay the correct battery box then.  

Questions:  Where is the proper mount point for the little rectifier?

Thanks!