Hi giboun,

I hate to say this, but don't be too quick to dismiss the altornator windingd theory.

My 3AJ Tenere became more and more difficult to start until it would only start on a brand new spark plug, even if the old one had only done 10 miles. The spark looked good with the spark plug rested on the side of the head, but it has a much harder time under compression.

A multimeter resistance reading of the coil that lives amongst the alternotor windings that supplies power to the CDI was about 10% lower than expected.
It took me some time to believe that this could be the problem, but eventually I replaced the alternator / CDI windings and it then ran perfectly for about 30 000 miles.

When I removed the windings I discovered that they were not original Yamaha ones but aftermarket ones that were supposed to suit a number of different bikes.

If I was you I would get a decent DMM that can measure in 0.1 ohm steps, unplug the CDI coils from the wiring loom and check their resistances against what Yamaha quote. I would also measure between them and 0V / frame - there should be extremely high resistance. If all is correct I would not consider replacing them.

also suggest getting the thing that you can fit between a spark plug and it's cap, that flashes when it sparks. This way you can check the plug under compression. They are very cheap anmd available from car accessory shopr.

Hope this helps.

If you need the resistance figures, let me know and I will find them out.

Mark