I have an AT2 that the electric start worked perfect, but it would not charge. Spun me around but at the end I ended up finding melted terminals in the voltage regulator, something I don't see in your photos. So, lesson learned: electric start will work, and charging system may not.

I 100% verified I had a charging system problem using the service manual inspections, especially the "full field" Initially, that test failed, even though the electric start worked. I replaced the brushes, and then that test passed as the manual stated, when full fielded I had DCV beyond 12V+ in a big way at under 3,000 revs. That's when I went further, removed the cover of the voltage regulator and found melted parts.
 So, adjustment - wise in the manual the regulator probably doesn't get "out of adjustment" until someone "put's it out of adjustment." 

If I were you, I would file the contacts in the voltage regulator since you have the cover off, make sure they are clean, use a drying spray cleaner like brakeclean, blow dry and slide paper between the contacts when done. Then I would do the full field step in the shop manual, because, if the alternator won't output a charge then you have to start at brushes, brush connections, and alternator connections.

Yes, the electric start field coils and brushes are not used for charging.  Two systems that share an armature.  Following the Yamaha test procedures from start to finish has never failed me in finding the issue.

From the 1969 Yamaha Shop Guide to Theory and Maintenance (can be found in the Tech Library)

 




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Sorry I have been slow to respond to all this - I haven't been getting notifications so didn't realise anyone was responding 

Thanks you for all the advice. I will check out the regulator operation although I am still not convinced the dynamo is producing enough ummph to make the regulator kick in.  I'll get back with a report

A couple of tips...  the older manuals tend to explain things in more detail.  In this case the early AT1 manual might be better than the AT3 manual regarding the generator.

The 1969 Shop Guide goes into more of the theory...  I think that's where I learned how the generator itself provides the power to the generator field coils.  (Yamaha calls it a "self exciting" generator) And how the regulator points open to keep the generator from overcharging when RPM goes up. So if the normally closed points in the regulator are dirty or somehow not making good contact when closed, you won't get any or much output.  So the regulator doesn't "kick in" as you imagine it does...  it "kicks out" to prevent overcharging.

I'd give the manual steps another shot...  I've never had following the procedure fail to identify and ultimately fix the problem if I went through the process without skipping anything.  I've always used the early manual.

If you want, post up pictures and descriptions as you go through the steps... 

This passage from the 1969 shop guide makes me smile because I've been guilty many times:

 




 

I will document the steps and post them sometime. Hopefully this week.