Weak CDI coil
I have a 1988 3AJ Tenere and when I bought it in 2000, unbeknown to me it was fited with aftermarket alternator windings, that incorperate the coil that powers the CDI and others that tell the CDI when to fire.It was a difficult starter and nothing I did realy improved it except a brand new spark plug. If I fitted a new one in the morning and rode until lunchtime it needed a new one to start in the afternoon! Eventually I replaced the windings with a second hand set of Yamaha ones and it became a good starter. Prior to this it ran fine once it started, if it started.
This year I acquired a friends 3AJ Tenere to replace my crashed & worn out one.
This one has always needed a tip-top battery to start if it has stood for a week or more, which is not a situation that I was prepared to live with. I have a so-so battery (according to hydrometer readings after charging) which would not start this bike until I replaced it's alternator windings with those from my crashed bike. The ones that I replaced on this occasion did look like the original Yamaha part.
On both occasions I got what looked like a good spark fron a spark plug rested on the outside of the cylinder head, and a gizmo that connects between the spark plug and the plug cap suggested it was firing inside the combustion chamber too. But presumably it wasan't quite enough to start a cold bike.
I can't explain why but it certainly seems to me that the coil that provides the power to the CDI does go week and result in a spark not quite strong enough to start a cold engine.
I would reccomend caution if you are concidering aftermarket windings.