I think andy is on to something, I googled around and found this
Generally speaking:
The biggest advantage to magneto ignition is that it is simple and reliable.
The biggest problem with magneto ignition is that it is simple and reliable.
E gap or efficiency gap (points setting)
Magnetos work best and deliver the hottest spark when the energy inductance to the coil caused by the rotating magnetic shaft is interrupted at the strongest point. This interruption is done by adjusting the points against a cam to cause them to open at just the right moment. Points that open sooner (smaller gap setting) or later (larger gap setting), are less efficient, and produce less of a spark than those tuned to the most efficient specified setting. This point gap varies by manufacturer but is generally not less than .012" and rarely greater than .025" (see maintenance manual.
Points fail when the condenser fails, by causing the transfer of metal on the face of the points that changes the E gap. Also the fiber rubbing block on the points can wear from corrosion on the cam, and lack of cam lubrication. Eventually the points do not open, and spark ceases from the magneto.
Over a long service life and from constant heat and cooling of the magneto, the rotor shaft may loose its magnetism. Or the coil may begin to break down. These failures are often noted in magnetos where they start well "cold" but the engine becomes hard starting once it warms to operating temperature, or after it becomes heat soaked. The lesser magnetism or failed coil results in a lesser spark, and harder starting. Pretty simple stuff.
http://www.luscombesilvaire.info/endowment/pop_topics/magneto_mysteries_exposed.htm
The guys at the Yamaha shop were trying anything rather than using logic, no spark check the carb? I don't know how to fix this but at least I have somewhere to start
