Again, AC voltage regulator does not regulate the battery charge voltage.  

Anyway, you're there with sounds like a frankenstein wiring harness or something.  My gut feeling still says maybe somehow battery is backfeeding to source coil due to melted/shorted wires or someone's "creative" wiring mods.  

(Twice I've seen a Yamaha magneto ignition deliberately and incorrectly connected to battery power by someone who thought it should be that way)

That's all I have...  except to caution you about voltage readings.  The "peak" numbers are important BUT can't be read accurately by most meters.  So keep that in mind if you didn't know.  

That doesn't look like a factory Yamaha ignition source coil either.  That could easily be the problem if coil specs not matched to the system it could run hot.  

A few more days of testing everything we can think of. (By we, I mean everyone that I have roped in at this end, at this point)
At this point everyone is stumped. Completely. 

There is about 37V AC on the brown wire at the stator loom connections. 5V on the Red/White.

Everything seems to be pointing towards the flywheel magnets being done. Somehow.
Its the only thing that makes sense, but somehow I doubt that it is.

I guess I need to source another flywheel to find that one out...
I assume they are not interchangable at all. A lot of LC flywheels about but not much for MX's that isn't knackered.... (F3T252 instead of 251)

But there is no other way to tell if it is bad magnets without substituting in another one to see if anything changes...

When this doesn't work I guess the entire stator is being torn down completely for a full rewire.Its the only other thing that makes the slightest bit of sense.
either its not generating the voltage or its leaking somewhere. On the plate itself.

Ignore me if I'm off the case, as on my useless fone. In my opinion 37volts is about half of what you need to throw a spark from your cdi stator. 5 volts from the trigger would trip it ok.

RT325, the problem with stator voltages always has been that you have a good "peak" meter and know how to use it.  We have no idea how this voltage is being measured and with what method or tools.  

I'm not going to re-read the whole thread but from memory we've been given several different readings on the same components for ohms and volts already.  It was also said the ignition source coil was OEM Yamaha and from the pic it's obviously not.  So it's really hard to diagnose when the data keeps changing...  For example. if the 37 volts was measured on an AC scale with a standard RMS meter, it might be about right?  

And of course I might be mixing up threads and my apologies if I am.  

The coil is genuine Yamaha now. But it wasn't. That was a picture of why I thought it needed replacing.

Its been complicated by the fact the old coil that tested open circuit was able to be fixed as it was the sub-standard lead put on it. Once that was replaced it worked again. And it throws exactly the same amount of voltage as the NOS Yamaha one. It was swapped back to see if the new coil was a dud.

The measurement is off of a borrowed Fluke 117. Best I could find. So yes. Probably standard RMS. The old set of voltages were off something with a far slower sample rate.

The resistances are unchanged. And I believe they are correct to within +-10% for a MK2 system.