Yeah okay, well that sounds like you've ruled out all most of the basic things.
I've had this before with a faulty ignition coil. These can still be bought brand new from Yamaha and I highly recommend going for genuine coil over an aftermarket one. The aftermarket one I had led me on a wild goose chase trying to figure out the intermittent fault.
You can measure the coil to see if it's within tolerance, what I was finding was that from cold it would work a treat, but once under load and warmed up, it would fail to fire above 4k RPM.
So it could be a worn out ignition coil, however unlikely that may seem.
Other than the stator/pickup, there really isn't a lot more to these engines to get them running.

But still check those connections anyway to make sure they haven't vibrated themselves to pieces.



