Hello Vintage Yamaha Enduro forum.
I once again darken your door, seeking opinions on what exactly could have gone wrong with my bike this time.

THE BACKGROUND CONTEXT.
Feel free to skip this wall of text. But it might be useful to know exactly how the current sequence of events happened.

A few years back I had issues with my bike frying a source coil. This was eventually figured out and replaced. And all has been right with the world for the last two-ish years. (With that bit at least…)

I feel that the current issues can be traced back to about April this year.
The entire DC charging system appeared to have quit. Upon tearing it down the damage was pretty severe. Our best guess is the voltage regulator had let go and fried just about everything hooked up to it. (Battery, Flasher relay, regulator, rectifier).
So I priced out replacement parts. I figured it was cheaper in the long run to install a rex's 12V conversion kit while I was at it, and that was that. Another 300 miles of fairly happy sailing.

However.

About a month ago I was on my way back home and suffered some form of engine failure at some traffic lights.
After some prodding about with the plug and fuel system we determined that there was a spark, fuel and that it still had compression. Just that it didn't want to start. It could be made to occasionally catch with a push start but it was impossible to keep it going.

My working theory at the time was that while there was a spark it must not be a good one as it’s the only thing that made sense.

I then began the fun task of pushing it home rather than trusting breakdown to arrive anytime soon. 8 miles, at 11:30pm.
At the top of one of the larger hills about 30 minutes later, I decided to see if push starting it would work, as it had sort of worked earlier but failed to keep running. So I gave it half a turn richer on the idle screw and hoped for the best. This somehow worked so I was able to limp it the last 6 miles home. (Saving me about 2:30 of walking).
THE PROBLEM SO FAR: for those skipping ahead

After giving everything a once over it seemed ok. Nothing seemed out of place.
But when trying to start it the spark had disappeared completely.
Working back through the system everything that could be tested checked out. Apart from the source coil. Again.
Upon extraction it appeared that it was fried even worse than the first one. Completely open circuit and blackened. Which would  seem to be the obvious answer as to why the spark has disappeared.  Almost exactly how it went down last time.

So two weeks were then spent waiting for a genuine Yamaha source coil to turn up.

This was then fitted. And no spark.
So the new coil was checked. Continuity. 314 ohm. Which is where it should be.
Then the pulse coil. Continuity. 10.3 ohm. Which is where it should be.

We then figured that it must be further up the system and that a new rex's CDI would be required as we had no way to test if the existing one had given up somehow. This did exactly nothing to rectify the problem.

There is no earth fault that we can find.
The ignition coil itself checks out at 12 ohm and is only a few years old as it was replaced last time.

It seems as if the CDI is not triggering and putting out any spark voltage to the ignition coil.
Which does put the suspicion on the pulse coil. Which checks out on a meter and does appear to put out about 2-10 volts. The new source coil is putting out 12-20 volts so that seems fine.

I thought that I would ask here for input as to other things that it could be, before I go dropping $200 on a pulse coil that may or may not fix this.
(After $160 for the 12V, $140 for the source and then $100 for the CDI in the last 3 months… My wallet can’t take this.)

Thanks in advance.

Welcome back & I'll have to have a long read tonight, but on the face of it I'd think the flywheel crank key had let go. Or if it's an aftermarket system with no key then it's slipped with the same result putting timing way out. But I think I read no spark now so I'll have a long read. To edit I see 12-20 volts on your source but I'm used to 160 volts on source coils but that's on a peak meter so 80 on a normal one. But I'm not sure what system you have so take my post with a grain of salt & I'm just talking of what im used to.

12 ohm coil for a cdi?

Might be a dot missing--like 1.2 ohms for the plug coil primary winding.

Seems the measurement I read off there is through the plug cap to earth so +5k.

Going by my notes from last time was replaced with the correct 1Ω primary and a 6Ω secondary. So its about right with the the cap I think. Within 10%, just.

 

More prodding.

It seems to be at a point now that the pulse coil that didn't seem do be doing much, is now. After going over the factory wiring and redoing all of the joints. That has about 5V on it now when hand cranked. Which I think should be enough.

There was also an issue with the source coil wire that was found as well. Turns out that under the kapton sleeve there was quite a mess.
Someone decided to use almost all of the aftermarket coil wire and cut down the loom I guess.
Anyway. That wire had a pretty bad cold joint and insulation that had clearly not been happy about the heat. Its fixed now.

There is a still a problem somewhere as the source coil appears to only be putting out 8V when cranked by hand.
By the time it makes it through the CDI its about 3V.

Which I think means that either the replacement NOS source coil that measures fine on a meter is somehow bad or that there is a massive drain/leak somewhere leading up to the CDI despite the fact that part of the loom not only tests ok but is currently bypassed just to be sure.

It seems to us. That there is no reason why it should be doing this now.

The new source coil is putting out anywhere between 18 to 37v. This is probably nowhere near enough. It should be about 200v?

The pulse coil has also decided to stop working again.

So its down to:
Fried pulse coil.
Dud source coil straight out the bag.
De-magnetised flywheel. Somehow.
Or a mix of these.

Its also sparking again. But very, very infrequently. Usually on the first revolution and then no more.

Electrical is hard enough to troubleshoot in person.  I haven't been saying anything because so many parts of this story don't make sense and/or are not clear.  

Plus the minute someone says "Rex's" I tend to pull back.  I love that they are trying to make parts.  Not really a fan of what I've seen sometimes when someone has an issue with one of their products, especially if you don't live in the UK.

Your bike should have three source coil windings and you keep talking about the "source coil" as singular without identifying exactly which circuit you are talking about.

Along with the 3 source coil windings, there are basically 3 separate electrical systems.  Stator AC coil to power CDI (brown wire).  And a combined-core stator AC coil with two separate windings.  One winding to power the AC headlight circuit (yellow wire) and one winding that is half-wave rectified to charge the battery (Green or Green with stripe wire).  

For practical purposes, these circuits are separate and independent of each other.  

In your initial description, you said the battery and several battery-powered circuit items "fried" along with "the source coil".  The suspicion mentioned was the voltage regulator.  It is not clear at all which of the three source coil windings went bad.

Several issues.  One is that the stock voltage regulator is AC only and connects only to the headlight circuit.  If the regulator went bad, you'd lose the headlight. Regulator does not have anything to do with battery charging circuit.

If regulator melted the stator windings for the headlight circuit somehow, then since the battery charge windings are on a common core, it could have fried the battery charge circuit windings.  

What doesn't make sense is other components going bad like the battery.

Ignition source coil is COMPLETELY separate from the lighting/charging source coil.  You could remove the lighting/charging coil and the bike would still run just fine.   (You could instead completely remove the ignition source coil from the stator and if you found a way to spin the flywheel, the headlight and battery charge would work fine, just no spark)

Stator coils don't tend to turn black and fry like you're describing unless something like the battery back-feeds the stator coil.  My guess is you may have a bad (shorted) rectifier or a short in the wiring harness someplace.  Maybe even some well-meaning person connected battery power to the CDI somewhere or there's some melted/shorted wiring hidden.  

Questions:  Exactly which source coil is bad?  Do you have a working fuse (or circuit breaker may have been standard, it was in the US) at/near the battery?  Has your rectifier been tested?

Final comment is that magnetos sort of run on "magic".  While the battery charge and lighting coil are not directly involved or connected to the stator ignition source coil, all the stator coils are powered by the same spinning magnets.  There is only so much power those spinning magnets can produce and that power is shared by the three stator source coils.  If somehow the lighting coil starts pulling more power, that leaves less power for battery charge and ignition.  So even if not directly electrically connected to each other by a wire, they are in the same magnetic field and do affect each other.   A bad lighting coil can draw enough power to cause ignition issues.  


 

I think I assumed that the battery charges off stator AC and not the headlight AC.That might be a large part of my confusion.

My loom is a bit "special" because it seems to be part MX and part LC. Which come from it being an October of 82 extremely late run out model. Which is why I do not have a wiring diagram that is 100% accurate to this bike. They are also not the easiest diagrams to follow at the best of times.

Anyway.
The most recent damage looked something like this. Open circuit which explains the no spark.
Edit: Its just been put back in to see what happens and is apparently working again. Despite looking like this.
Stator Plate
And by working I mean still only putting out 18v and no spark.


The rectifier was replaced along with the regulator when it was converted to 12v. Those parts have about 300 miles on them.
The old rectifier seemed to be ok but that was only a few years old as it was replaced last time it had issues.
The old regulator was out of spec, putting out slightly too much voltage which is probably what fried the battery.
There is still a fuse, and it has been modernized to accept blade fuses.


Re: Rex. Its mostly a convenience thing being UK based. Nearly the same price as 40 year old used components on eBay so makes sense.
I have also seen how they get with people when there is a problem. Things were somewhat patronizing for a bit before they even considered it might be their fault. (Which it was)

 

If there's no spark that problem is un related to the charging side. The burnt looking coil--maybe only looks that way--is your ignition source. Resistance without researching I'm thinking should be about 350 ohms. Ac voltage output to 'that wire' in the mag loom should be about 80, or 160 on my peak meter at Kickstart speed. Ignore me if I'm off the case as not read back yet but just going by your comment 'still no spark'. Happy to be corrected if someone's got all the proper resistances & voltages.